Here's my take if your compression truly is bad in both those cylinders. The shop doing the job didn't properly diagnose the cause of the misfire in the first place. They GUESSED it was a fuel injector issue, when all along it was a compression issue. You don't just all of a sudden lose compression on two cylinders.

But, I agree with @gamefreakgc . Get the compression numbers from the original shop and maybe even bring it to another shop for a compression test to confirm the findings. At this point, I'd have very little trust in that original shop. The 3RZ engine is known to burn up valves because the valve lash gets too tight.