So I went out today to start the car because it had been sitting for a couple weeks. I played with the pwm settings and was able to get the car to idle when warm without me pressing the gas. I also decreased the req_fuel and scaled the VE table to get more resolution to make it easier to hit the afr targets.
I took the car for a quick spin to get a log of that problem I'm having when the car gets into boost. The problem is I'm getting a sync loss, and the sync loss reason says 2 which corresponds to missing tooth at wrong time. I'll post the log later, but it's happening all the time around 2800-3000 rpm. I currently have no noise filtering enabled though. I guess I could try turning that on and see if it solves the problem.