Advice! I'm good a giving that, even when I'm not asked for it.
So, my advice would be to buy/find the proper tools for the job. Set yourself up a nice area to work, and clear it of anything that might get in the way. Be patient, and work through things before you do any drilling, screwing, or soldering. Specific advice:
1.) When drilling, use a drill press when possible. You will get best results if your drilled holes are straight.
2.) Get some real nut files and possibly some fret files.
3.) Get the right wattage soldering iron.
4.) Use the right type of solder.
5.) Buy quality parts, don't skimp.
6.) Make sure you get the neck on straight

Straight edges are your friend.
7.) Make sure the pickups you choose will work with where warmoth puts the routes. I noticed the Sadowsky pickups I purchased for my P-J project didn't line-up quite right.
8.) Use masking tape to protect the paint when you are working.
9.) Route your own truss-rod access route. The Warmoth one doesn't go deep enough.
10.) Use a template when you route!!
11.) Your time costs money, don't forget that

It took me about 10 hours total to put mine together, and I still didn't finish the nut. I had one of the nickle alloy nuts from Warmoth, those are hard to work with.
12.) If you decide to sell, you won't get your money back.
13.) Have fun.