I need some insight as this is odd and I'm hoping someone has dealt with or come across similar before.

1997 cobra. Stock except; msd wires, k&n filter, 4.10 gears, off road h-pipe, and SCT tune by Steeda.

Car has a hesitation, more so when it's cold at the 3250 rpm range where IMRC would open. When I check visually both sides open when cold or warm at the proper range. Cables are free moving and seem to function as they should.

Car has a slight pause when accelerating at this magic 3250 rpm. The odd part is I can hear a clicking coming from my PCM area in my passenger panel when I pass this rpm it clicks when accelerating and decelerating past it.

No codes are present. I looked a day ago and it showed a p1516 and a p1519 I believe. It's why I checked the imrc but functioned as they should via test. I cleared codes and drove 100 miles since without any codes.

Car still has clicking noise and slight hesitation at 3250 rpm. Gets less when car is warm. I took car and put back to stock tune and it still does it. Car actually seems to run the same with stock tune vs. Steeda set tune.

Any ideas and help are appreciated.