Sounds like the fpr is fine and set, the maf is good, tune is good.

Just needs some fine tuning.

With the ls intake and relocated maf, the tune probably needs to be tweeked, which is normal.
Plus, you're regulating the fuel better than factory, so that's one variable on why the truck is a tad rich.

Just have your tuner lean it out, give him the ltrim values, that'll help.