I understand if you buy a copy of SH4 Gold on a DVD there is no SecuROM to have all this fun with. I use a Direct2Drive version as well and I wish I hadn't bought it. I have mitigated all the bad effects but one: won't run if I forget to shut Process Explorer down.
The one-time use install key I sidestep by copying all the files from my Wolves of the Pacific directory to a directory on another drive I call SH4 Pristeen. I do this before I even run the game. Then I write protect SH4 Pristeen, every file in it. That renders it impossible to run that version by mistake. Then when I get mod soup, I just delete everything from my Wolves of the Pacific directory except for JSGME, MultiSH4 and my MODS subdirectory. then I copy everything from SH4 Pristeen to Wolves of the Pacific. And the last step is write enabling the whole shebang in Wolves of the Pacific.
Instantly, without reinstalling I have a virgin copy of SH4 ready for me to make more mod soup with. And I don't care because at any time I can restore it all in five minutes without uninstalling and reinstalling. If you write a batch file and hook it to a shortcut on the desktop you can do this with a single double-click!
Easiest way to do this within a batch file is to use
xcopy!