Possible timing issue

I asked about this same car a few months back. Had to replace head gasket in it and afterwords had trouble getting the exciter rings realigned. I bought the timing lock down kit for this engine and used it to get the rings reset. Now, the car starts and will run smooth as a new engine for approximately 2 minutes, then it starts idling really rough and you can hear the lifters knocking. After a short while from that point the car just dies. I’ve noticed the battery isn’t holding a charge while it sits even for just a couple days. So I know it needs to be replaced. I’ve attached my code reader to the car and it still shows the same dtc’s it had before I replaced the head gasket, at which time I also replaced the turbo. The dtc’s I’m getting are, 1. Engine misfire. I put new plugs and coil pack in the car 2. Camshaft position sensor on exhaust side not plausible. I used the lock down kit to reset them. 3. Turbo waste gate solenoid circuit. My helper forgot to attach the wiring harness when we first put the car back together. 4. Knock sensor. I didn’t do anything with this. All 4 of these codes show as permanent codes, but won’t they reset after starting the car enough times? I’m suspicious of a possible electrical issue because my son ignored a coolant leak until it finally blew the head gasket.