I wouldn't be discouraged, just jump in, that's what I did. There's nothing more rewarding that playing a guitar that you built with your own hands.
I've built 2 so far and almost completed my 3rd. It is challenging but having great tools and knowledge makes all the difference.
A great resource is www.projectguitar.com
A book that I read which really helped initially used to be found at this website, but the link didn't work for me. www.buildyourguitar.com
The hardest part in my opinion is the neck. Measurement of the fret spacing has to be extremely accurate and fretting/leveling etc is quite hard. The body is somewhat easier however measurements still must be very accurate specifically bridge placement. Finishing is no picnic either but patience pays big dividends.
There are a couple of ways you can go that I know of:
1. like Hikey Mikey said above - order a kit and assemble it, this doesn't have quite the same appeal to me as building a complete custom guitar yourself.
2. build the body and finish it then buy a used neck or have a custom neck built for you. This virtually guarantees playability provided you've measured the scale length correctly and placed the bridge the correct distance from the nut. I recently had a custom strat style neck built for me by Warmoth. www.warmoth.com
. It was about $450 but nicer than any Ibanez, fender, or Jackson neck and totally custom to my specs.
3. Build the body and neck - a challenge but extremely rewarding. Note, you can buy precut fretboards. A great guitar tech can fret level and set it up to play beautifully. Here is the last one I did, it's a kind of JEM like guitar http://www.flickr.com/photos/guitvai1/
Parts can be sourced from Warmoth Guitars, Stew Mac and your local guitar store (pickups, pots, knobs) to name a few.
Wood: - Homedepot, Lowes etc only have building grade lumber. You will have to go to an exotic wood store or find it on the net. There are quite a few places that sell instrument grade wood on the internet. This is a local store luckily for me that I buy at for example, http://www.exotic-woods.com/
Most important is a good router - stay away from cheap routers that only take 1/4" shank bits, you'll just be frustrated by the choppy results.
Drum and Belt sander
Good measuring straight edge.
A lot of time and patience but it pays off. It's kind of addictive and the more you practice the better you'll be (like anything).
Cost: It ain't cheap. Expect to pay $1,000 to $1,500 in parts if you are like me and demand Ibanez Edge or Original Floyd Rose etc. It adds up quick
Pickups: $100 each x 3 + $300
Knobs, neck screws and misc: $50
Finishing supplies: $200
Custom neck (optional!!): $450 (Warmoth)
Sounds like a challenge I'm sure but nothing worth doing in this life is easy!! (sorry about the philosophy)