I tried updating and then eventually deleting possibly offending modes, I tried adjusting the batch file to not look for mods mentioned immediately before and after the above section, but no success.
I found a pre-downloaded collection of standard BWP mods from another source and using that folder as a base collection of mods, I re-installed BG1 and BGII in the same process as detailed in the first post. Once again, I manually found and extracted missing mods. Right now the batch file is installing and it has long passed the point where I was crashing. Fingers crossed.
Having the correct versions of the mods appear to have fixed the crashing issue. I was never able to find a way to fix the patch check without editing the batch file.