Texotic

I'll second the comments on the pinion angle. That's the only thing associated with the driveline that would have changed with the lowering. Nothing that I can thing of in the FRPP kit should increase NVH noticeably, so that's all I can come up with. and Adjustable UCA or a set of Adjustable LCA's will get you the pinion angle adjustment you need and with the LCA's you'll get a large drop in wheel hop that I'm sure you have after adding the Whipple.

Sleeper_08

Here is a link that provides some explanation on pinion angle, LCAs and the UCA http://www.cherod.com/mustang/HowTo/LCA%20_adj.htm

It is unclear what has been changed on your car but as suggested above you may have affected the pinion angle when you lowered the car.