Yeah I had this problem a few years ago and solved it in the following way:
Remove stupidly long screws. Discard
Attach baseplate to pedal using duct or electrical tape (I used electrical as when removed it should not take any paint from the housing with it).
Apply velcro to base of pedal. VOILA.
I promise you, in 4 odd years of lugging around my pedalboard, not once has the baseplate come loose from the wah, being only held together by tape.
It's that or cut down your screws, or take them to a hardware store and ask for the same design but a a few cm shorter.
OR:
Wah Pedal Mounting Plates - Dunlop, RMC's, Vox, Budda and others.