Figured out the problem, turns out that I removed speffects too late. I used CSGEdit to allow myself the correct weapons and I think that might've fixed that problem.
Now my problem is that while I can use everything, almost nothing's in my weapons pool.

I should be able to fix that by playing the next mission...or with a bit of hex editor hacking

Edit: Oh, no, the EXE version doesn't work because I never installed Freespace 2. Just copied the VPs and EXEs. That means there's no uninstall data in the registry, which is what all programs use that try to auto-find the FS2 directory.