Nice work you have done there!
I just did the same conversion my self last week, using JB Racing flywheel and Spec clutch (Supercharger plans).
But after re-mounting the exhaust I noticed the forward exhaust support/clamps (in front of the cat) didn't fit as they used to mount to the auto trans crossmember. Did you buy new clamps, or have I just overlooked where it's supposed to mount?
and by the way, you mentioned you had some noices from the flywheel below 1500rpm, what kind of sound?
My 540 makes this hissing/blowing sound which disappears when i pass about 1400rpm, more power=louder noice. Could it be the same noise you are experiencing?