This is a quick rework of nematode's list combined with mine, and grouped into Classes. The class ship is bold, if it has no "=NAME" the ship already exists in game. My only major break from nematode's list is Hiyo, she looks more like Taiho, IMO.
http://www.combinedfleet.com/taiho_c.htm
http://www.combinedfleet.com/hiyo_c.htm
I also think Yubari might be better as the DD Akizuki, the minelayer has far less weaponry, though the down side it as a DD, it will hunt you. Also, Shimakaze has to be Akizuki, not Fubuki she was over 3000 tons! 
I could actually quickly make cloned versions set to be type=6 for those.
OTOH, nematode's choice of Kuma for Tenryu was clearly superior.
I haven't finished grouping the DDs, I'll edit this later. BTW, they are arranged in the large list, and within class by date, hence the odd looking order. (also because combinedfleet.com does it this way and it's easier to copy the list, lol)
Battleships
BB
Fuso
BB Yamashiro =BBFuso
BB
Nagato =BBFuso
BB Mutsu =BBFuso
BB
Kongo
BB Hiei =BBKongo
BB Kirishima =BBKongo
BB Haruna =BBKongo
BB
Ise (pre-rebuild)
BB
Ise (post-rebuild) =BBIse Late War
BB Huyga (post-rebuild) =BBIseConv
BB Hyuga (pre-rebuild) =BBIse
BB
Yamato
BB Musashi =BBYamato
Heavy Cruisers
CA
Furutaka
CA Kako =CAFurutaka
CA Aoba =CAFurutaka
CA Kinugasa =CAFurutaka
CA
Myoko =CATakao
CA Ashigara =CATakao
CA Nachi =CATakao
CA Haguro =CATakao
CA
Takao
CA Maya =CATakao
CA Chokai =CATakao
CA Atago =CATakao
CA
Mogami (pre-rebuild) =CATakao
CA
Mogami (post-rebuild) =CAMogami
CA Mikuma =CATakao
CA Suzuya =CATakao
CA Kumano =CATakao
CA
Tone =CAMogami
CA Chikuma =CAMogami
Light Cruisers
CL
Tenryu =CLKuma
CL Tatsuta =CLKuma
CL
Kuma
CL Tama =CLKuma
CL Kitakami =CLKuma
CL Oi =CLKuma
CL Kiso =CLKuma
CL
Yubari =MLOkinoshima (I might "BP-clone"
Akizuki to be a CL for her instead)
CL
Nagara =CLKuma
CL Isuzu =CLKuma
CL Yura =CLKuma
CL Natori =CLKuma
CL Kinu =CLKuma
CL Abukuma =CLKuma
CL
Naka
CL Sendai =CLNaka
CL Jintsu =CLNaka
CL
Katori =MLOkinoshima
CL Kashima =MLOkinoshima
CL Kashii =MLOkinoshima
CL
Agano
CL Yahagi =CLAgano
CL Noshiro =CLAgano
CL Sakawa =CLAgano
CL
Oyodo =CLAgano
Fleet Carriers
CV
Akagi =CVShokaku
CV
Kaga =CVShokaku
CV
Soryu =CVHiryu
CV Hiryu
CV
Shokaku
CV Zuikaku =CVShokaku
CV
Unryu =CVHiryu
CV Amagi =CVHiryu
CV Katsuragi =CVHiryu
CV
Hiyo =CVTaiho (alt Shokaku, but look at them, it
looks more like Taiho IMO)
CV Junyo =CVTaiho
CV
Taiho
CV
Shinano =CVTaiho
CVL
Chitose (post-rebuild) =CVETaiyo
CVL Chiyoda (post-rebuild) =CVETaiyo
CVL
Hosho =CVETaiyo
CVL
Ryujo =CVETaiyo
CVL
Ryuho =CVETaiyo
CVL
Shoho =CVETaiyo
CVL Zuiho =CVETaiyo
Escort Carriers
CVE
Taiyo
CVE Chuyo =CVETaiyo
CVE Unyo =CVETaiyo
CVE Kaiyo =CVETaiyo
CVE Shinyo =CVETaiyo
Destroyers
Momi (Old DD)
DD Hasu (
Momi Class) =DDMinekaze
DD Kuri (Momi Class) =DDMinekaze
DD Tsuga (Momi Class) =DDMinekaze
DD Sanae (Wakatake Class) =DDMinekaze
DD
Wakatake =DDMinekaze (Old DD)
DD Asagao (Wakatake Class) =DDMinekaze
DD Fuyo (Wakatake Class) =DDMinekaze
DD Karukaya (Wakatake Class) =DDMinekaze
DD Kuretake (Wakatake Class) =DDMinekaze
DD
Minekaze
DD Sawakaze =DDMinekaze
DD Okikaze =DDMinekaze
DD Hakaze =DDMinekaze
DD Yakaze =DDMinekaze
DD Akikaze =DDMinekaze
DD Shiokaze =DDMinekaze
DD Yukaze =DDMinekaze
DD Hokaze =DDMinekaze
DD Tachikaze =DDMinekaze
DD Nokaze =DDMinekaze
DD Namikaze =DDMinekaze
DD Numakaze =DDMinekaze
DD
Kamikaze =DDMinekaze
DD Harukaze =DDMinekaze
DD Asakaze =DDMinekaze
DD Matsukaze =DDMinekaze
DD Yunagi =DDMinekaze
DD Hatakaze =DDMinekaze
DD Oite =DDMinekaze
DD Hayate =DDMinekaze
DD Asanagi =DDMinekaze
DD
Mutsuki
DD Fumizuki =DDMutsuki
DD Kikuzuki =DDMutsuki
DD Kisaragi =DDMutsuki
DD Mikazuki =DDMutsuki
DD Minazuki =DDMutsuki
DD Mochizuki =DDMutsuki
DD Nagatsuki =DDMutsuki
DD Satsuki =DDMutsuki
DD Uzuki =DDMutsuki
DD Yayoi =DDMutsuki
DD Yuzuki =DDMutsuki
DD
Fubuki
DD Shirayuki =DDFubuki
DD Hatsuyuki =DDFubuki
DD Murakumo =DDFubuki
DD Shinonome =DDFubuki
DD Usugumo =DDFubuki
DD Shirakumo =DDFubuki
DD Isonami =DDFubuki
DD Uranami =DDFubuki
DD Ayanami =DDFubuki
DD Shikinami =DDFubuki
DD Asagiri =DDFubuki
DD Yugiri =DDFubuki
DD Amagiri =DDFubuki
DD Sagiri =DDFubuki
DD Oboro =DDFubuki
DD Akebono =DDFubuki
DD Sazanami =DDFubuki
DD Ushio =DDFubuki
DD
Akatsuki =DDFubuki
DD Hibiki =DDFubuki
DD Ikazuchi =DDFubuki
DD Inazuma =DDFubuki
DD
Hatsuharu =DDShiratsuyu
DD Ariake =DDShiratsuyu
DD Hatsushimo =DDShiratsuyu
DD Nenohi =DDShiratsuyu
DD Wakaba =DDShiratsuyu
DD Yugure =DDShiratsuyu
DD Harusame =DDShiratsuyu
DD
Shiratsuyu
DD Shigure =DDShiratsuyu
DD Murasame =DDShiratsuyu
DD Yudachi =DDShiratsuyu
DD Samidare =DDShiratsuyu
DD Yamakaze =DDShiratsuyu
DD Kawakaze =DDShiratsuyu
DD Umikaze =DDShiratsuyu
DD Suzukaze =DDShiratsuyu
DD
Asashio
DD Oshio =DDAsashio
DD Michishio =DDAsashio
DD Arashio =DDAsashio
DD Natsugumo =DDAsashio
DD Yamagumo =DDAsashio
DD Minegumo =DDAsashio
DD Asagumo =DDAsashio
DD Arare =DDAsashio
DD Kasumi =DDAsashio
DD
Kagero =DDAsashio
DD Kuroshio =DDAsashio
DD Oyashio =DDAsashio
DD Hatsukaze =DDAsashio
DD Natsushio =DDAsashio
DD Yukikaze =DDAsashio
DD Hayashio =DDAsashio
DD Maikaze =DDAsashio
DD Isokaze =DDAsashio
DD Shiranuhi =DDAsashio
DD Amatsukaze =DDAsashio
DD Tokitsukaze =DDAsashio
DD Urakaze =DDAsashio
DD Hamakaze =DDAsashio
DD Nowaki =DDAsashio
DD Arashi =DDAsashio
DD Hagikaze =DDAsashio
DD Tanikaze =DDAsashio
DD Akigumo =DDAsashio
DD
Yugumo =DDAsashio
DD Kazagumo =DDAsashio
DD Makigumo =DDAsashio
DD Makinami =DDAsashio
DD Takanami =DDAsashio
DD Naganami =DDAsashio
DD Tamanami =DDAsashio
DD Suzunami =DDAsashio
DD Onami =DDAsashio
DD Fujinami =DDAsashio
DD Kishinami =DDAsashio
DD Hayanami =DDAsashio
DD Kiyonami =DDAsashio
DD Okinami =DDAsashio
DD Hamanami =DDAsashio
DD Asashimo =DDAsashio
DD Kiyoshimo =DDAsashio
DD Hayashimo =DDAsashio
DD Akishimo =DDAsashio
DD
Akizuki
DD Teruzuki =DDAkizuki
DD Suzutsuki =DDAkizuki
DD Hatsuzuki =DDAkizuki
DD Niizuki =DDAkizuki
DD Wakatsuki =DDAkizuki
DD Shimotsuki =DDAkizuki
DD Fuyuzuki =DDAkizuki
DD Hanazuki =DDAkizuki
DD Yoizuki =DDAkizuki
DD Haruzuki =DDAkizuki
DD Natsuzuki =DDAkizuki
DD
Shimakaze =DDAkizuki
DD(E)
Matsu =DDMutsuki ? Hard to do this guy.
Patrol Boats (ex-DDs)
Patrol Boat No. 1 (ex-Minekaze Class Shimakaze) =DDMinekaze
Patrol Boat No. 2 (ex-Minekaze Class Nadakaze) =DDMinekaze
Patrol Boat No. 31 (ex-Momi Class Kiku) =DDMinekaze
Patrol Boat No. 32 (ex-Momi Class Aoi) =DDMinekaze
Patrol Boat No. 33 (ex-Momi Class Hagi) =DDMinekaze
Patrol Boat No. 34 (ex-Momi Class Suzuki) =DDMinekaze
Patrol Boat No. 35 (ex-Momi Class Tsuta) =DDMinekaze
Patrol Boat No. 36 (ex-Momi Class Fuji) =DDMinekaze
Patrol Boat No. 37 (ex-Momi Class Hishi) =DDMinekaze
Patrol Boat No. 38 (ex-Momi Class Yomogi) =DDMinekaze
Patrol Boat No. 39 (ex-Momi Class Tade) =DDMinekaze
Patrol Boat No. 46 (ex-Wakatake Class Yugao) =DDMinekaze
Patrol Boat No. 102 (ex-Clemson Class, USS Stewart) =DDClemson
Fleet Oilers
Fleet Oiler (Auxiliary) Akebono Maru =OLNippon
Fleet Oiler (Auxiliary) Genyo Maru =OLNippon
Fleet Oiler (Auxiliary) Itsukushima Maru =OLNippon
Fleet Oiler (Auxiliary) Kenyo Maru =OLNippon
Fleet Oiler (Auxiliary) Kokuyo Maru =OLNippon
Fleet Oiler (Auxiliary) Kyokuto Maru =OLNippon
Fleet Oiler (Auxiliary) Nichiei Maru =OLNippon
Fleet Oiler (Auxiliary) Nippon Maru =OLNippon
Fleet Oiler (Auxiliary) Shinkoku Maru =OLNippon
Fleet Oiler (Auxiliary) Toei Maru =OLNippon
Fleet Oiler (Auxiliary) Toho Maru =OLNippon
Gunboat (Auxiliary) Nagata Maru =KMSSKinposan
Hospital Ship Naminoue Maru =PLKiturin
Kaibokan Hachijo =MSNO13
Kaibokan Ishigaki =MSNO13
Kaibokan Kunashiri =MSNO13
Kaibokan Shimushu =MSNO13
Kaibokan Shimushu =MSNO13
Minelayer (Auxiliary) Tenyo Maru =KLCSNagara
Minelayer Itsukushima =MSNO13
Minelayer Kamone =SCSubchaser
Minelayer Okinoshima =MLOkinoshima
Minelayer Shirataka =MSNO13
Minelayer Tsubame =SCSubchaser
Minelayer Tsugaru =MLOkinoshima
Minelayer Yaeyama =MSNO13
Minesweeper W-1 =MSNO13
Minesweeper W-10 =MSNO13
Minesweeper W-11 =MSNO13
Minesweeper W-13 =MSNO13
Minesweeper W-14 =MSNO13
Minesweeper W-15 =MSNO13
Minesweeper W-16 =MSNO13
Minesweeper W-17 =MSNO13
Minesweeper W-18 =MSNO13
Minesweeper W-19 =MSNO13
Minesweeper W-2 =MSNO13
Minesweeper W-3 =MSNO13
Minesweeper W-4 =MSNO13
Minesweeper W-5 =MSNO13
Minesweeper W-6 =MSNO13
Minesweeper W-7 =MSNO13
Minesweeper W-8 =MSNO13
Minesweeper W-9 =MSNO13
Netlayer Hatsutaka =DDMinekaze
Repair Ship Akashi =MLOkinoshima
Repair Ship Asahi =MLOkinoshima
Repair Ship Yamabiko Maru =KLCSNagara
Seaplane Tender (Auxiliary) Kamoi =OLNippon
Seaplane Tender (Auxiliary) Natoro =OLNippon
Kamikawa Maru
Seaplane Tender (Auxiliary) Kamikawa Maru =KLCSNagara
Seaplane Tender (Auxiliary) Kimikawa Maru =KLCSNagara
Seaplane Tender (Auxiliary) Kiyokawa Maru =KLCSNagara
Seaplane Tender (Auxiliary) Kunikawa Maru =KLCSNagara
Seaplane Tender (Auxiliary) Kinugasa Maru =KLCSNagara
Sakitu Maru Class (converted to transports in 1942)
Seaplane Tender (Auxiliary) Sagara Maru =KLCSNagara
Seaplane Tender (Auxiliary) Sanuki Maru =KLCSNagara
Seaplane Tender (Auxiliary) Sanyo Maru =KLCSNagara
Seaplane Tender Akitsushima =CVSChitose
Seaplane Tender
Chitose (pre-rebuild) =CVSChitose
Seaplane Tender Chiyoda (pre-rebuild) =CVSChitose
Seaplane Tender Mizuho =CVSChitose
Seaplane Tender Nisshin =CVSChitose
Subchasers
Subchaser Ch-1 =SCSubchaser
Subchaser Ch-10 =SCSubchaser
Subchaser Ch-11 =SCSubchaser
Subchaser Ch-12 =SCSubchaser
Subchaser Ch-13 =SCSubchaser
Subchaser Ch-14 =SCSubchaser
Subchaser Ch-15 =SCSubchaser
Subchaser Ch-2 =SCSubchaser
Subchaser Ch-25 =SCSubchaser
Subchaser Ch-26 =SCSubchaser
Subchaser Ch-27 =SCSubchaser
Subchaser Ch-28 =SCSubchaser
Subchaser Ch-29 =SCSubchaser
Subchaser Ch-3 =SCSubchaser
Subchaser Ch-33 =SCSubchaser
Subchaser Ch-4 =SCSubchaser
Subchaser Ch-5 =SCSubchaser
Subchaser Ch-6 =SCSubchaser
Subchaser Ch-7 =SCSubchaser
Subchaser Ch-8 =SCSubchaser
Subchaser Ch-9 =SCSubchaser
Submarine Depot Ship (Auxiliary) Heian Maru =KLCSNagara
Submarine Depot Ship (Auxiliary) Nagoya Maru =KLCSNagara
Submarine Depot Ship (Auxiliary) Rio de Janeiro Maru =KLCSNagara
Submarine Depot Ship (Auxiliary) Santos Maru =PLKiturin
Submarine Depot Ship (Auxiliary) Yasukuni Maru =KLCSNagara
Submarine Depot Ship Chogei =MLOkinoshima
Submarine Depot Ship Jingei =MLOkinoshima
Torpedo Boat Chidori =DDMutsuki
Torpedo Boat Hato =DDMutsuki
Torpedo Boat Hatsukari =DDMutsuki
Torpedo Boat Hayabusa =DDMutsuki
Torpedo Boat Hiyodori =DDMutsuki
Torpedo Boat Kari =DDMutsuki
Torpedo Boat Kasasagi =DDMutsuki
Torpedo Boat Kiji =DDMutsuki
Torpedo Boat Manazuru =DDMutsuki
Torpedo Boat Otori =DDMutsuki
Torpedo Boat Sagi =DDMutsuki
Torpedo Boat Tomozuru =DDMutsuki
XPCs:
Armed Trawler will work (I have one made with japanese crew and weapons ready to go).
Armed Tug will work (I have this as well).
IJ ARMY "Carriers" Really "plane ferries." (these should all be reset to zero air groups since planes flew off ONCE to land bases)
Nigicu Maru = Akitsu Maru
Shimane Maru = Akitsu Maru
Otakisan Maru = Akitsu Maru
Yamashiro Maru = Akitsu Maru
Chigusa Maru = Akitsu Maru
Kumano Maru = Akitsu Maru
On the Armed Merchant Cruisers below, couldn't we use the German Aux Cruiser (NAMC in the Sea folder)? All we need do is add it to the roster.
http://www.combinedfleet.com/Tokusetsu%20Junyokan!.htm
Of course the NAMC is about half the size of a real armed merchant cruiser.
Armed Merchant Cruiser Aikoku Maru =KLCSNagara
Armed Merchant Cruiser Akagi Maru =KLCSNagara
Armed Merchant Cruiser Awata Maru =KLCSNagara
Armed Merchant Cruiser Hokoku Maru =KLCSNagara
Armed Merchant Cruiser Kinryu Maru =KLCSNagara
Armed Merchant Cruiser Kiyosumi Maru =KLCSNagara
Armed Merchant Cruiser Kongo Maru =KLCSNagara
Armed Merchant Cruiser Noshiro Maru =KLCSNagara
Transport Aobasan Maru =KLCSNagara
Transport Arabia Maru =KLSSHakusika
Transport Arizona Maru =KLSSHakusika
Transport Asakasan Maru =KLCSNagara
Transport Asosan Maru =KLCSNagara
Transport Atsutasan Maru =KLCSNagara
Transport Ayatosan Maru =KLCSNagara
Transport Borneo Maru =KMSSBiyo
Transport Brisbane Maru =KMSSBiyo
Transport Cheribon Maru =KMCSAkita
Transport Chifuku Maru =KMSSBiyo
Transport Chile Maru =KMSSBiyo
Transport China Maru =KMSSBiyo
Transport Clyde Maru =KMSSBiyo
Transport Delagoa Maru =KLSSHakusika
Transport Fushimi Maru =PLHorai
Transport Fuso Maru =PLHorai
Transport Hawaii Maru =KLSSHakusika
Transport Hayo Maru? =KMSSBiyo
Transport Hirokawa Maru =KLCSNagara
Transport Hiyoshi Maru =KMCSHeito
Transport Hokkai Maru =KLCSNagara
Transport India Maru =KMSSBiyo
Transport Johore Maru =KMCSHeito
Transport Kamo Maru =PLKiturin
Transport Kamoi Maru =KMCSAkita
Transport Kansai Maru =KLCSNagara
Transport Kashii Maru =KLCSNagara
Transport Katori Maru =PLHorai
Transport Kenkon Maru =KMCSHeito
Transport Kinka Maru =KLCSNagara
Transport Kinugawa Maru =KLCSNagara
Transport Koyu Maru =KMSSBiyo
Transport Kumagawa Maru? =KLCSNagara
Transport Kunitama Maru =KSSSKasagisan
Transport Kurohime Maru =KMSSBiyo
Transport Kuwayama Maru =KMSSBiyo
Transport Kyushu Maru =KLCSNagara
Transport London Maru =KLSSHakusika
Transport Macassar Maru =KMCSAkita
Transport Matsue Maru =KLSSHakusika
Transport Meigen Maru =KMSSBiyo
Transport Mexico Maru =KMSSBiyo
Transport Miike Maru =KLCSNagara
Transport Moji Maru =KMCSAkita
Transport Myoho Maru =KMCSHeito
Transport Nagano Maru =KMCSAkita
Transport Nako Maru =KLCSNagara
Transport Nichiran Maru =KLCSNagara
Transport Nichiryu Maru =KMSSBiyo
Transport Nikki Maru =KMSSBiyo
Transport Nojima Maru =KLCSNagara
Transport Ohio Maru =KMSSBiyo
Transport Oigawa Maru =KMCSAkita
Transport Oregon Maru =KMSSBiyo
Transport Oridono Maru =KMSSBiyo
Transport Risshun Maru =KMCSZinbu
Transport Ryoyo Maru =KMSSBiyo
Transport Ryuun Maru =KLSSHakusika
Transport Sado Maru =KLCSNagara
Transport Sagami Maru =KLCSNagara
Transport Sakura Maru =KLCSNagara
Transport Sanko Maru =KMCSAkita
Transport Sasako Maru =KLCSNagara
Transport Shinai Maru =KMCSAkita
Transport Shinsei Maru No. 1 =KMSSBiyo
Transport Shinshu Maru =PLHorai
Transport Shiraha Maru =KMSSBiyo
Transport Shunko Maru =KMSSBiyo
Transport Suez Maru =KMSSBiyo
Transport Sumatra Maru =KMSSBiyo
Transport Tacoma Maru =KMCSZinbu
Transport Taibun Maru =KMSSBiyo
Transport Takao Maru =KMCSAkita
Transport Tamahoko Maru =KLSSHakusika
Transport Thames Maru =KMSSBiyo
Transport Toho Maru =KMCSHeito
Transport Toho Maru =KMCSAkita
Transport Tosan Maru =KLCSNagara
Transport Unknown Maru (Kinkai Maru?) =KMSSBiyo
Transport Unknown Maru (Samaran Maru?) =KMCSAkita
Transport Unknown Maru (Shinkaha Maru?) =KMCSAkita
Transport Unknown Taifuku Maru No. 1 Class =KMSSBiyo
Transport Unyo Maru No. 2 =KMSSKinposan
Transport Venice Maru =KMSSBiyo
Transport Wakatsu Maru =KMSSBiyo
Transport Yamaura Maru =KLCSNagara
Transport Yawata Maru =KSCSTaihosan
Transport Yokohama Maru =KLSSHakusika
Transport Yuri Maru =KLSSHakusika
Transport Zenyo Maru =KLCSNagara