12s are no problem with the stock bottom end. Can you run 12lbs of boost, well that may be pushing it a little bit but I have seen it happen before. Just not for long. The ARP studs will be better than the stock bolts, but mearly a band-aid for the bigger problem.
With what you already have just add the blower, a good tuner and some time on the dyno and you will have a different car. Add heads, intake and cams and you should be close to what your stock bottlom end can safely handle.
I have a friend with a Pypes x pipe and it hangs way too low. Drags the ground in some driveways and all speed bumps. I have heard of this being a common problem with Pypes.
When you work on a car you do encounter a certain amount of "Murphy's Law" but what you are going through seems a bit excessive. It is really hard to find a shop that you can trust that does good work. If you do find one they stay wrapped up and it takes forever for them to get to your car and...
Auburn diff and Moser axles in mine, holding up to launching on slicks hard. I've seen 8.8s run in 8 second cars before. They will hold up to just about anything.
If you have them welded in I would keep an eye on them as they work. They usually don't like people to do that but you are paying for it so you should be happy with the end result. Alot of the guys that work at the local shops (not saying all) don't really care about the quality of the work they...