I'm probably rehashing most of what's already been said here but many of these of these are personal, hard-learned lessons:
1.) Unless you already have access to a shop full of tools, your first*(edit) build will most likely cost you well beyond what it would to just buy an instrument. If you are just doing it to save a buck, you probably won't. Do it because you like woodworking and/or you want something unique.
2.) There are many ways and tools one can use to achieve a desired outcome. Educate yourself in the use of power
AND hand tools and pick the one that makes you feel most comfortable. Power tools do damage a lot faster.
3.) Consider experimenting with cheaper woods and use templates and jigs.
4.) Make a full size drawing. And incorporate all your parts into the design - down to the electronics cavity. Stick to the plan - if you change something - change it on your drawings also. AND: make sure your routes (pickups/electronics) on opposite sides of your instrument don't conflict.
5.) Spend some time planning your glue-ups and dry fit everything before you start putting glue on it. Related: you can NEVER own too many clamps.
6.) The most important thing in an electric guitar is a stable, playable neck. Consider those constraints first and don't get hung up on 'tonewoods' for electrics. I've seen good sounding guitars wrapped in duct tape, have plexiglass bodies or fiberglass necks. In the end - the only thing all of those instruments had in common were playable necks and good electronics.
7.) If you are designing a bass, put some thought into where the upper horn/strap button goes. Thick necks and small bodies can create neck dive - if you don't plan ahead, by the time you realize you have neck dive - it will probably be too late.
8.) Eccentric body styles (especially by the 'bridge' strap button) don't sit well in most guitar stands.
9.) Accept that you will make a mistake. Probably a couple.
See also: The Matrix - "everyone falls on their first jump." Then again, maybe you are "The One."