New LS1 Owners - Newbie Tech - New Tranny/Stall Now Exhaust Popping

My transmission blew on my A4. I went from having the PI3600 stall to a stock stall ~1800 and no longer having my shift kit installed as well (yes, this car is slow now).
My exhaust starts popping/slapping between 2000rpms until 2200rpms, other then at those rpms it is never heard. I can only hear it in 1st and 2nd gear. This problem never occurred before the new transmission, and doesn't occur on the highways.
I can avoid it completely if I keep my foot out of it.

Thanks in advance,

Travis

Any DTC's on? Check and make sure no wires got caught and pinched between the bellhousing and engine block upon reinstall.

No codes on my scanner. I noticed today if I manually shift it, which I never do, it will not do it. Only when it is getting ready to shift from 1st to 2nd at 2k rpm. It seems as if it has too soft of a shift, and sounds similar to an exhaust leak, but once again only for that rpm and during the 1st to 2nd shift. I was thinking of putting a shift kit back in, hoping it may fix this issue.

Thanks for the help.