Towards the discussion of pre-maf stuff not causing issues...
I chased an issue for a while after my stage 2 install that resulted in whacky idle fuel trims. Checked everything, even had the car smoke tested (only the second thing I've paid someone else to do on the car to this point)--nothing. Turned out to be my aFe dry flow air filter. It just wasn't sealing completely, so a small amount of air was getting pulled into the box there. It was pre-maf, but still causing an issue.
Take that for what it's worth. If you remove the lower box, I would at the very least plug the hole that it creates.