Update...
So I went back and forth with Unitronic a bit. They recommended I test for any vacuum/boost leaks. Did a pressured smoke test, no leaks. They also sent me a revised version of the Stage 2 IS20 tune (not sure what they changed), but that didn’t fix the issue either.
So after much frustration and tons of troubleshooting, I decided to just swap back in my stock IS12 turbo and then flash back to the standard Stage 2 file. Zero issues now. No misfires or EPC light during shift, and wastegate duty cycle is back where it should be. Car is WAY slower, but I’m happy not having to worry about this problem anymore.
My best guess is that for whatever reason, my transmission wasn’t getting along with the extra torque and power the is20 was providing, and the tune or transmission wasn’t seeing what it‘s expecting. Not enough knowledge on how the transmission and tune work together, but it’s really the only thing I can think of.