DearthVader,
I'm no pro, but I don't think you can have too much vacuum. The vacuum merely affects the dead side of a diaphragm and provides extra 'muscle' that gives you the power effect. There is a brake return spring that overcomes engine vacuum and pulls your pedal back up.
If you were to disconnect and plug the vacuum line, ideally you should have great brakes...just a lot of pedal effort. The vacuum thing is different than a slug of air or faulty proportioning valve or some other mechanical problem.
I'm not real clear from your post exactly what your problem is. Is it 'hard' pedal with good brakes or mushy, funky brakes. Unhook and plug the vacuum line (engine side) and see what manual brakes feel like...is the problem you describe still there?
Stuart