Possible AFR problem?
 

I have a 1991 bone-stock N/A and I was wondering if I put a big cone air filter on if it could screw up the AFR. Thanks in advance!

Nope. All of the air is still metered by the "air-flow meter" or AFM (right after the filter or stock airbox) which would compensate for any added "air". However, you won't gain any power from replacing the stock airbox with just a cone filter. To gain any sort of power you'll have to create a "cold-air" intake or CAI. Do a search for "CAI" or "intake" if you want some ideas or descriptions of what would be a better alternative.