The holes not lining up is a common problem with replacement pickguards. The worst I ever bought was an Allparts P-bass replacement-- the pickup routing and holes were way out of position. It may have fit some variation of P bass perfectly, but not the one I had.
Some pickguard makers will want to work off a tracing, others will want you to send in your original. Then there's Chandler (Pickguard Heaven), which has supposedly exact patterns for many different variations (see
here). There's a pic of their tort in the materials section. I've seen some of their guards in person before, but not the tort.