You kind of built your mix backwards. Do it like
100_FalloftheRisingSun_Ultimate_v1.8
101_FotRSUv18_FixPak
AddInModzPak_18
Nippon_Maru_v1.9b_FotRSU
Nihon Kaigun v1.3a_FotRSU
Combined Roster
304_NoJapaneseAirRadar
399_OAKsHudGauges
Fleetboat_Interior-Officers_Quarters_FOTRSU_v1.7_EN
FI-OQ_FotRSU_v1.8f_upcPatch
Also, you left out the first lines of the JSGME export, which gives your install path, so what is the path to your modded game, and had you deleted the Save folder ("C:\Users \UserName \Documents \SH4" by default) before playing the modded game?