P0303 Code after Engine Rebuild

[CL1CK]

Hello all, I'm currently scratching my head as well as the shop the car is currently at so I thought I might try here and see if anyone has seen these issues.

For some backstory the crankshaft thrust bearing failed at around 88,000 miles which caused a lot of crank walk and tore up the inside of the block requiring me to order a new short block and rebuild the heads among some other miscellaneous parts.

I am currently experiencing an intermittent misfire on cylinder 3 that only occurs on cold start and clears up after engine idle drops to below 1k RPM. The idle is also lower than what it has been around 600-750 RPM range (before rebuild was 800 RPM). It's been to the shop already for this issue in which they replaced the plug and coil for that cylinder, but the issue keeps occurring. The weird part is, I will drive the car for 200+ miles before it'll come on after I leave the shop.

*Note the car is stock other than a muffler delete the previous owner did, but I had no CEL codes and no issues with the engine before the rebuild.

If anyone has any ideas, I'd like to hear them. The shop right now thinks it's possibly a leaking injector, but I am currently at a loss.

[RZNT4R]

Idle is normal, mine idles at bang on 600 warm.

Misfires don't have to come from the spark plug or coil, it can be fueling or mechanical. If it takes 200 miles for it to come on then it's going to be a pain in the ass no matter what it is, but since it happens on cold start (when it has to run richer) I'd lean on the fuel side of things. I don't know if they know, but with a decent scan tool you can +/- the injection amount to force it into having the issue.

For example, if it's missing during startup enrichment because an injector isn't injecting enough, you +++ the injection amount and the one clogged injector and it's cylinder run fine while the other 3 run filthy rich and miss.

You can test both DI and PI like this, so if it's fuel related, the tools are there to make some sense of it.