The p0016 and p0344 are new after doing the work. I had a miss on #3 before the work and found a trashed on cam, lifters, and stretched timing chain.

Yeah then I would think you're off on the timing.

I am going to replace the crank sensor tomorrow just to see if that does anything. If not I am going to have to check the timing chain.

I just can't see how I would be off on the timing. I lined up the arrows and put the chains marks at the gear marks. Seems pretty straight forward.