May be lose under torqued leaking connector tube. Retorque the tubes while waiting on your EFI programmer.
It will still shutter on stock tune, even unplugged my Edge monitor. The new EFI live tunes didn’t help or worsen the issue. My plan is to start at cyl 1 and work my way back. I haven’t noticed any fuel leaks, if I do have one at the tube my guess is I would have some fuel in my oil, I may drain it first just to verify.
What is lift pump supply psi and rail pressures commanded vs actual, when issue happens ?