That's a good suggestion, you should know what's in each of those holes before moving forward after this discovery.
yes, and it this point, trust absolutely nothing the previous mechanic touched. Recheck and baseline anything they touched as much as possible as you proceed with fixing your problems.
if something they touched could potentially be a cause for your issue, treat it with suspicion until you can rule it out.
I think you're dealing with something simple that has been overlooked or misunderstood.
trouble shoot the basics, start with and eliminate the cheap low hanging fruit before opening the engine and removing the head.
work on one potential problem at a time. be certain you understand the outcome before moving on to the next one.
eg, get injector install sorted, then test drive.
if that's made a difference to the miss, move on to tuning the fuel pump settings. recheck timing with the correct tool. if this isn't 100% correct, consider checking the pump timing gears were aligned correctly.
if all good, tune boost and fuel settings. this is simple enough, but is quite a process in its own right.
you can tune this yourself if so inclined.
if you do it as a novice tuner, expect to tune, test, retune, test, repeat multiple times. there's good info on here about the tuning process.
you might just be amazed at the results
compression test was good. was a leak down test done too? if both these are good, there should be no reason to remove the head base on what you have told us.