There's nothing in mounting flange area except polyurethane, so you can chop it off and it won't hurt the electrics. There isn't any reason you can't sand down the mounting and get them in the cavities lower. More drastic would be making the routings for the pickups deeper (but do mind you don't punch through the back!).
Sorry John, but the material isn't thermoplastic.
You can buy sets of pickups, and even if you don't replace the humcanceller at the same time (you really should) you should at least buy the correct matched one and keep it safe for when you do have a chance to crack the old one out. Email me if you want any other purchasing details.