Ya adding the short shifter made it really hard to get a clean shift the way the intake was setup. Lengthening the pipe toned down the throttle so it's not so jumpy.
I have noticed that the idle rpm of Stage2 is a tiny bit higher than with IE Stage1 and there is a ton of torque just off idle. Yes it is a bit harder to sync with the clutch maybe this is what you are dealing with, I come up and match a bit quicker now to deal with it, a bit like the old 911s.
BUT the Stage2 Tune was designed for minimal 6 inch runner length of the IE SRI now
I have it working with the long runners of the Stock IM.
IDK about that Shifter Mod, I have to pass for now.