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I did a 5.3 swap on my 98 Tahoe... the engine has a noticeable miss during idle and flashing check engine light with code P0300..I have only scanned so far with a OBD program on my phone... I have checked all my connections.... thought it was a injector and I changed it with the same results....
Check for vacuum leaks. I once had the foam under the intake that got partially wedged between the head and intake runner. If not vacuum leak, did you do a re-learn on the crank position sensor? CAS (Crank Angle Sensor) Learn (aka CPS learn)needs to be done any time you disconnect the PCM for any significant amount of time, or service the crank sensor. It sounds like you are working on a fresh LS swap, so CAS learn should be done before throwing any more money at the issue.
Other stuff. Where is your MAF? Sometimes poor idle airflow across the sensor gives you bad readings and causes issues. There is actually a lot of info on the interwebs on the P0300 issues, have a look around, but do a CPS/CAS relearn first.
Figured it out today,, put it on a scanner,,, problem with connector on one of the coils..............