So! Deleted the second copy and used S3F to create a copy of the confirmed functional steam version again, and it still wouldn't run (same error). I am assuming there's something else in play there but getting sick of trying to troubleshoot when I have one version that does work anyway.
Download the GWX packages and try to run it on my steam install, it errors saying I've modded it and as such it can't run. I go back into S3F and undo the 4g patch, and in theory the H.sie patch (size did not go back down, so I'm not sure it did anything). GWX still refuses to run.
Wipe out my steam version again, and re-install, and run GWX first. Same error preventing install.
Now that's odd, I never touched it after the install... Start the GWX patch again and go a little slower this time- the default path is pointing to a SH3 folder in my documents, not the steam/steamapps directory.
OKAY redirect the installer to the correct directory, and it runs this time! Check to make sure it's functional- OMG A DIFFERENT LOADING SCREEN! Close out and pop open S3F again, hit it with H.sie and 4g- pop it open again- STILL RUNNING!
I did the artillery exam, and aside from being confused that now there's only HE shells, and struggling with some oddities that I'm not sure if is learning curve, or actual issues- but hey, it's solid progress.
Confusion after all this: compared to my experience in stock, my orders seem to take unusually long to be recognized. Does one of these mods add crew reaction time in the mix? Also twice after changing my speed while surfaced the boat refused to go and I couldn't figure out why. I had to submerge and resurface to jog it into allowing movement.
Edit: Also holy cow it takes a lot of HE shells to sink ships. I know your deck gun isn't supposed to be a massive killer or anything but jeez that training mission was a lot of sitting there just hitting the space bar.