I had to replace the pickups in an old Columbus Jazz Bass a year or two ago and had a similar problem - the original pickups had radiused corners and the body was routed to match, the replacement pickups had squared corners and wouldn't fit...
I managed to (carefully with a little heat) prise the pickups from their covers and swap them around - the pole spacing was slightly different but I managed to get 'round that with a little judicious filing to open the pole apertures allowing the new pickups to be rehoused in the original covers. It all worked out quite well and maybe this method would work for you too..?