Well, after about 3 hours and 2 broken Snap On tools, I've determined the best solution would be to take it to a muffler shop and have them mess with it. Ahh, this was a great DIY project, I'm glad I started this now instead of just selling the bypass pipes as I was originally going to do.
What do you think it will cost for them to remove 2 bolts and a nut and bolt the bypass pipes on? I'm thinking $100 or so.