sorry if i insulted you in any way, but these questions need to be asked, ( we dont know you personally yet) guys go and rebuild these engines and they fail asap on them, then they learn about the machine shop work needed.

when done right, as you already know your dumping up to 2500 into the rebuild, and stock internals will hold 500 hp from a turbo. why we most here will opt for a used engine.

being we now know your are a mechanic now, id think maybe a leak down test might shed some light on things. if a valve seal didnt not push off, we've seen a few guys lately that had a seal pop off for no good reason.

could also be a stuck open injector fouling out the plug.

or maybe even a bad icm or coil. you got the little crank harness ground bolted on the coil bracket right?

have you tried a crank relearn yet? sounds like you must have a tuner on hand or at least a tech 2. if you changed pcm's or the bin file for the pcm even if its not showing a code for the crank relearn it can still help.