Actually, I have not drilled the bottom of the map box yet because of the clearance issue. Yesterday afternoon I decided to back out the screws on the top panel, then put a few screws into the face of the instrument panel containing the map box (instead of the cleko's). Next, I tightened all the top cowling screws again. There was some improvement. Now only the left upper corner of the box hits the firewall.
The firewall checks out to be straight, so that does not appear to be the cause of the issue.
I think I might just shave a bit off the offending corner of the map box and move on. I guess its not worth losing too much sleep over.
Thanks for the suggestions,
Alex