MAF check engine light and transmission help

[heeroyuy01195]

I hope this is in the right spot but here goes, a few days ago I had my car in the shop to have the clutch changed due to grinding going from 3rd to 2nd gear. When I received the car there was a knocking noise when I moved off, pulled the car apart and found that my Transmission mount was the problem. During the process of removing the battery and the tray to inspect and reinstalling it, I picked up a check engine light (nothing related to the intake was removed aside from cable ties). The OBD reader said it was an issue with the MAF (or at least that's what the mechanic told me it said). He couldn't clear the code and recommended I just pull the negative terminal for a bit to reset the car. I did that and I still have the CEL. When the car starts it will hesitate a bit, sputter, then finally start up. While driving there is virtually no power when trying to accelerate.

I pulled the car apart on my own to check if anything might have been forgotten during reassembly but everything checks out and i still have a CEL. I removed the MAF to take a look if it might have been damaged but it looks fine (I can't recall but is the side facing the filter supposed to be slightly black?). I can't think of anything else to check. I reinstalled the stock intake (which seems to delay the check engine light from coming on for a bit) but that didn't stop it. The car's been sitting for about an hour without the negative on now, going to check it tomorrow to see if it goes away. Any other ideas? Anything I should check that I might have missed?

On a side note, the car still grinds from 3rd to 2nd. Changed to a Competition Clutch (stage 1) and Royal Purple transmission fluid, any thoughts on this matter? Thanks in advanced!