Custom operating systems and crankshaft relearn?

Is their any problems relearning the crankshaft position sensor when failing the MAF on a 3 bar setup?

There shouldn't be. I've had a few of LS1's that show 0.4% on the TPS sensor in the scan tool when at idle, and have had to manually make it show 0.0% to do the CASE relearn.
Just follow the CASE relearn procedure and see how you go.

So you are saying you have relearned the crankshaft position sensor with MAF codes in the back ground?

Just P0102, it shouldn't trigger a MIL if you failed the MAF as per the speed density tutorial.