Turns out my knocking/driveability issue had to do with the injector and COP pigtails. Couple had the stupid little tab broken and would not stay on. I took out all the plugs, regapped, put in new pigtails where broken, and it is at least firing on all cylinders now.
I still have the problem with the car suddenly going into safe mode (wrench icon), though. I thought it was TPS or throttle body related, but I've replaced the throttle body, TPS, and TAC, and it is still happening. Datalogging has narrowed it down to what looks like an EVAP or venting problem with the tank (ref: my other thread on this).