I am have a 2001 525i that misfires and backfires through the intake manifold. I connected a scanner and have multiple codes: 202,203,227, 228,238,239,240,242,243. Do you have any idea what the cause of this misfire/backfire is?

Not sure about E39's, but my car is at the dealership with multiple misfires and rough start caused by improper intermediate levers/ lifters. Stealership repair cost was $6k..

Some of those codes can be as a result of an initial failure in O2 sensors; best to have a BMW saavy shop diagnose your car so you don't start replacing parts that are OK. Watch out for indys who replace part after part using hope as their diagnostic strategy. They may eventually fix the problem but only after replacing expensive parts that were OK to begin with.