V13dweller, just some thoughts ...
... when you started again, did you use the same player name as you had before and are the saves in the same location under that same name? Are you loading a previous save that's in the dock and not at sea? You mentioned that you don't even get to the pen, so I'm assuming this is the case, but am asking anyways. Also, did you have a backup of that SH5 folder in My Documents in case the new install had over-written any of your settings? I remember having similar problems, because those settings didn't match after a reinstall. If the restore didn't work, I just started a new campaign to save the hassle.
How about starting a new campaign using a different name to make sure the game can start with your loaded mods. If that works, then it could be anything mentioned above or by other people.
I hope it works out ...