FWIW, the bigger exhaust diameter + different mufflers I'm sure has cost something on the low end. But I would be concerned about the fact that after the clutch was done and before the exhaust work (do I have that right?) you felt a difference.
I'm with Jeff. I would go over to zfdoc.com and look in the Q & A section about C-beam alignment. Heck, Bill is a stand up guy and always answers Q's if you e-mail him. I would do some checking up on the C-beam alignment just to be sure. JMHO.
Tom