never heard of a regulator issue on the B5, their windows just work. Sounds like it was just stuck somehow. If the motor thinks theres an obstruction it stops trying.
The manifold flange looks like it has been seriously warped, and someones buffed it flat to get it to seal. As we discussed before, these manifolds are junk, and you will have continuous issues with them.
If you really want to keep this setup going, i would be looking at a PSI Concepts cast manifold.