Figured I should update this since I got the car back now, it turns out that I didn't re-crack the intake. The shop forgot to reset the ECU after the fixed the vacuum leak. It's running much better now and haven't had many problems with it. It still has its 3.5k rpm stumble when it's cold (still working on getting the firmware version of the FIC) and every once in a while it will stall out immediately after starting (but once I get going it runs just fine). The shop agreed to take another look at the tune on Monday and see if they can't get it even better. Next up is the clutch/flywheel and 9.5psi!