Ok so I put a new mechbox on my m4 and now the screw that holds my stock on is 5/8s to fn long, do I just cut the screw and hope the mechbox re-threads the screw or what

Measure twice cut once and just clean the burr off the cut end. Make sure it threads in nicely by hand first then assemble it. Done this many times.. Dremels are fun at this point.. Smells good too!

I should be ok cutting an 1/8 - 3/16 extra off just so I only have to cut it once 'eh

yeah too much and you might not thread into the nut enough and strip it or too long and you have to tear it down again and recut it all over again.