Hello Matt,
I, like you, have greater joy than ability with guitar. I've started guitar making this year and I can help you with a couple of your questions.
I don't know where you can get kits, but e-bay is a good place to start. You can get separate bodies and necks from different folk, often for real bargains. I bought a decent strat neck for under $40. Check out this site for similar.
http://cgi.ebay.com/ws/eBayISAPI.dll?ViewI...0&rd=1&tc=photo
I'm carving my own bodies, so I don't know where you can get them, but I can tell you that wood with more closed grain is easier to paint. That would include alder (which is a pretty standard strat wood) which is a fairly cheap wood compared to others.
For good cheap pickups, look at the GFS range on e-bay (look up guitarfetish as the seller). There is a wide variety of styles of pickup which are very reasonably priced. Look at the reviews on Harmony Central too (http://www.harmony-central.com/Guitar/Data2/GFS_Pickups/) to see which ones suit your needs.
Guitarfetish also has some hand made knobs, but I don't know where you can get custom made ones. Remember that anything that is made especially for you will be MUCH more expensive, so you may be better off getting something ready made that is close rather than breaking your budget on knobs.
Good luck, and let us know how you get on with the project.
Brian.