Robert,
I dont know how a bearing issue would be causing a misfire, unless the piston slap was REALLY bad and then you would be loosing oil and it would sound like a bag of spanners in a washing machine.
What are you using to diagnose the issue? Is it a garage computer or a private VCDS / other ODB plug in unit?
It should be able to pinpoint where the misfire is coming from! I have seen reconditioned / reprogrammed injectors throw up errors in the past. Especially on remapped cars.
It might be worth getting a second opinion on the bottom end, as without hearing the car or knowing the fault codes, anyone could be throwing darts into the air and waiting to see what fault it picks.