Man, I just read all 7 pages, and it was really fun. reminded me a lot of all the questions I had going into my first guitar. A couple quick comments.
Pickups : Coolest (opinion obviously) lookin, and best sounding for a les paul = P90's. Try one out if you get the chance, they are great. When you read "single coil" don't think "strat sounding." P90's are mean!
Les Paul Jr's are the coolest guitars on the planet and make easier projects with only one pickup and no carved top. Joan Jet played a Jr that sounded amazing. So did Johnny Thunders.
My first guitar, I built the neck, and the truss rod. I had help (I wouldn't have known I had to temper the thing after brazing the head on it), but this board is a really incredible resource. If you've got your heart set on building something that'll be dificult, there's no reason you can't do it.
Good luck and best wishes. You've really got the treatment here. Sometimes people will only get answers that say "use the search function."
Can't wait to see pictures.
Billy Bones