Majority of ppl get an engine rebuilt, drop it into the car, and pray to god no issues arise. And if there are issues take engine back out or lean over fenders to take it apart been there done that. Basically you are about 5 steps ahead of the average Joe being engine has been dyno run, an issue was flagged and corrected, and engine run again on dyno to verify yes issue was resolved. Shop was transparent an f-up happened and it was fixed. So I would have a lot of confidence in that engine if I were you.
And yeah every project has hick ups unexpected issues crop up that is all situation normal. My two cents.