I'll just address the ones I know enough to help with.
Pickups: Humbuckers are what you want for that LP sound. As for the specific models, that's where it gets tough. There are a lot of manufacturers out there, some good, some great, but you'll find that price is often a limiting factor. Also, the style of music you like to play (or want to play) is extremely important to consider when choosing pickups. Personally, I love Bare Knuckle Pickups. I have about three sets so far, but the only humbucker by them that I have is the Nailbomb. I love it, it's fat, rich, and agressive. It's a higher output pickup, so it's more suited for modern type rock/hard rock/metal, but I think it can do more vintage sounds pretty well too. Bare Knuckles are great, and I haven't run across many people who don't like them, but they are pretty expensive (about $270-$300 for a pair of humbuckers). Check out the Mules for great 59 PAF tone. The best part is that you can send them an email telling them the sound you're after (be as specific as possible) and what type of guitar they'll go into and they'll tell you which of their models would work best.
Output jack: This one isn't too hard, just go with the 7/8" route. It's the proper size for a Les Paul. Just be sure to use a square jack plate, as those are the standard for Les Pauls.
Bridge route: Well first of all you'll probably want a Tune o Matic bridge route, if you want it to look like a proper Les Paul. As for compatibility with your wider nut width, I don't honestly know. I've always gone with the standard 11/16" myself. You should call Warmoth and ask if you need a wider spaced bridge for that nut width, or if a standard Tune o Matic will do fine. By the way, if you go with a tune o matic, check out the Gotoh or the Tonepros, they fix most of the problems with the original design.
Neck pocket: The 720 mod isn't necessary, I have a Warmoth guitar with no pickguard and no 720 mod and the fretboard doesn't feel like it's too far away from the body or anything. Without the mod the fretboard is only a few millimeters off the body, and keep in mind the fretboard doesn't actually overhang very far at all with a 22 fret neck. What I would recommend, however, is a contoured heel. It is definitely NOT vintage correct or anything you'd ever see on a Gibson Les Paul, but it is incredibly helpful in reaching those last couple frets and it's not something anyone else will ever see anyway, so it won't take away from the Les Paul vibe.
Stud install: If you are unfamiliar with the concept, the tune o matic bridge and tailpiece sit on posts (or studs) that are pushed into the body. It's not too hard to do yourself, but if you aren't confident you can have Warmoth do it instead for $10.
Battery box: You only need this if you're installing active pickups or a Ghost system or something similar. You probably won't need it.
Neck wood: Mahogany is a great sounding wood, but be sure to check out the exotic raw wood necks as well. Some of the woods Warmoth offers don't require a finish, such as Goncalo Alves, Rosewod, Wenge, Pau Ferro, Bocote, Canary, etc. I made the mistake of overlooking these woods the first time I ordered a Warmoth neck, and now I'm considering replacing that neck in the future now that I've experienced the raw wood necks. If you're looking to retain the LP warmth, you should probably stick to a Goncalo Alves or Rosewood neck. Wenge is a great neckwood too, but it's more midrange focused and possibly a little brighter. Don't be put off by that though, it can be good to mix a warmer body with a brighter neck to get a best of both worlds kind of sound. Check out the LP necks in the showcase, there are some beautiful all Rosewood necks, Wenge with Ebony, and a stunning Wenge with Macassar Ebony board:
http://www.warmoth.com/Showcase/Neck.aspx?i=LPN915&Body=1
Neck scale length: You didn't bring this up yourself, but this is important. Warmoth's standard scale length is 25.5". However, Les Pauls traditionally use a 24 3/4" scale length. Mostly the difference will be in the feel of the strings. A 24 3/4" scale length will make the strings a little easier to bend, but if you're an acoustic player the slightly greater string tension of a 25.5" neck shouldn't bother you. If you want a 24 3/4" scale length Warmoth makes a conversion neck that achieves this.
Fret size: This you'll have to decide for yourself. It's such a personal thing that you really just need to play a bunch of different necks and see what you like. Acoustic guitars tend to have medium to smaller sized frets I think, but playing an electric is a whole nother ball game. I personally love the 6100 frets. They are the biggest Warmoth offers, so if you are heavy handed you can push the strings out of tune, but I switch between those on my electrics and the small frets on my acoustic (with a much higher string tension) and even a bass and I don't have a problem lightening my touch for the electric. Whatever size you go with, choose STAINLESS STEEL!! They are very smooth and hard, much much harder than the standard nickle frets. This is important because they will last much much longer, meaning less fret levels (which are expensive) and less fret replacements (which are even more expensive and can only be done so many times before ruining the fretboard. If you combine the stainless steel with the 6100 size, you could go forever without replacing the frets, as long as you are ok with them getting progressively smaller over the course of your lifetime :icon_biggrin:
Tuner holes: Figure out what tuning machines you want, then get the proper size hole. I can't recommend the Gotoh 510 tuners enough. They are the smoothest, most accurate tuners I've ever used They don't look like standard Les Paul tuners, though :-\ I use the locking versions, but I play Strats with trems. You don't really need locking with a TOM, but it can make string changes faster. Check them out, they're great:
http://www.stewmac.com/shop/Tuners/Guitar,_solid_peghead_tuners/Gotoh_Tuners/Gotoh_Midsize_510_Tuners_with_Metal_Knobs.html
