You planning on doing something like this?
http://www.unofficialwarmoth.com/index.php?topic=3732.0
I can tell what NOT to do, I loaded this build up with a Rio Grande TX/BBQ set in the neck/bridge position, and put an SD Jazz pickup in the middle for something "different"...
Problem is, the Jazz pickup has so much lower output that it's practically unusable unless you make a change to the amp volume setting compared to the other two.
Whatever pickups you use, it's probably best to follow the lead of what goes in Strats stock, i.e., neck/middle pickup of similar output and bridge pickup hotter than those two.