The valves have been properly adjusted since I've had the car. No clue about before then.

Since the ECU controls timing and A/F, could this be a case of something else causing the ECU to over compensate (maybe a bad injector)?

 

It's possible, but I'd lean towards the idea that a previous owner had the valves out of spec for a bit. All it takes is running the motor for a little while with a valve out of spec causing excess carbon buildup. That buildup in turn will cause the valve to not seal properly, allowing combustion gasses to get past the valve and seat in turn burning both. It's never a bad idea to have your injectors serviced when performing major surgery like this anyway. Only costs about 20$ per injector from a number of the big name companies online and you'll end up with like new injectors in the end. Definitely worth it in my opinion.

 

Yeah, I planned on getting the injectors tested/cleaned. I have 4 from my old motor which I might do as well just to have some good spares.