A few things to check before thinking something is broken:
- 45sec is actually just a ballpark. Turn on VVT Exhaust in the logging and wait for it to start reading values. I've had this take over 1 minute before depending on temperature.
- "Dead pedal" is pretty common right after a flash, and seems to last longer on a cold car. If you aren't expecting it, it can feel like the car is about to stall out every time you put your foot down. This gradually goes away with 15-30min of driving as sensors calibrate.
- You do have a catless UEL, right? That's what is needed for Stage 2.