Engine sounds like a damn steam engine!

Last night, smooth and quiet. This morning its running smooth and quiet again. Drop it off to get the allignment done. Pick it up and its sounding horrible. Its making a chugging noise like a steam engine and is shaking noticeably. What's really making me scratch my head is nothing was done to the engine. It was all suspension work so why would the engine suddenly change? Once I am on the throttle it runs better but it still pretty rough.
Any thoughts?

sounds like the boys at the shop went racing

Big intake air leak somewhere. Check the SC tubes to make sure they didn't tweak one causing it to leak.

Ok its comming from the supercharger because the rotors are out of allignment and the back ends of them are rubbing. I have searched a number of times to try to find out the allignment specs with no results. Would anybody happen to know the spacing?

Those don't get out of alignment magically. Did someone have that blower apart?

Just over a year ago, probably 14 months, one of the guys in the SCCoWC ported my blower. Absolutely no problems until all of a sudden today they started acting up.

I dropped in some teflon rotors from a 99 gtp into a 95 blower. one alignment pin was in the wrong spot, so i had to pull one out, file the proper hole bigger, and drop the pin in the proper hole. Am I asking for trouble?