While these guys are arguing about what is best and how to do it ( ) I can offer you what I have done, as I am still a total newb. The books are a great source of info. Lots of reading though... I've built kits, from templates, and one completely from scratch. You can get by with basic tools for a lot of this. I'd throw in a recommendation though for this DVD: http://www.amazon.com/Complete-Custom-Elec...1396&sr=8-3
It goes step by step for making a guitar. Way more information than you need actually. Its nice too because when you start building your own you can skip to the chapter that you need and see how this guy does it. I think most of his tools suck but he builds a decent instrument with them so they can't be all that bad.
This forum is also great. I've been lurking here like you wouldn't believe. Forget about searching, just start reading all the threads and hope your head doesn't explode. Woodworking forums like sawmillcreek.org are also a great resource.
As crappy as they are, something like a Saga strat kit will serve you well if you've never built anything or don't do any of your own setup.