I've been talking with a couple tuners online, they said its not likely a tune issue since "tunes don't change, parts and engine conditions do". The car did run well and did not seem to have this issue up till a few weeks ago, so i can understand what they're saying.
I haven't found any tuners in my area that work on anything besides Hondas, either. So I'm either paying minimum 80/hr for troubleshooting at a shop or 500-800 to put it on a dyno and hope that the shop knows how to tune it properly.
I did take it out for another drive, seemed to run a bit better with the one code cleared off and the MAF cleaned.
I'm honestly not wanting to sink a ton of money into this engine/set-up. I was originally thinking of pulling the Vortech off and starting fresh slate with a KB kit, but I can do a coyote swap for less then it'd cost to get a KB set-up. And make more power, reliably, with better MPG.
So my long term (hopefully) plan for this car is a coyote swap. I had planned to do supporting mods to the suspension and k-member to better prepare the car for the eventual swap. Good thing is the 4.6 and the 5.0 share the share mounts. Doing this would allow me to gather supporting parts for the swap here and there when I stumble upon a good deal or sale.
Heck, I'd almost be tempted to pull the Vortech off if I felt it'd run ok without it.