Why are you so set on a Full Shred set? If I were you I would get the guitar the way I want it and then get pups to round it out....much easier and cheaper than changing out necks and such.
Why not with an Alder body and a maple neck and then experiment with pups string etc. to fine tune? There are a lot of great tones to get with that simple combo.
Let me try to understand... You're worried about messing up the resale value of a Les Paul by changing the pickups (which is something you can easily undo and get the resale value back) but you want to spend $600+ on a Warmoth?
I got news for you bro: Nobody buys used Warmoth guitars. If you're thinking about this guitar as an investment, a custom piece is NOT for you...actually, it IS for you, it's ONLY for you, and so nobody will be wanting to buy it from you...heh.
Besides: the Les Paul formula is tried and true, proven to rock out and sound great time and time again...and you already know of a model that you really like. You'd be saving yourself a lot of time and energy by grabbing a guitar you know you like, and tweaking the electronics to suit your wants.
Take it from somebody who's been there before man...my Warmoth is disassembled in a corner with no electronics to put in it, but my SG gets played daily and I love the stock pickup. It's not like I hate the Warmoth, it's just that I payed a ton of cash for it, spent almost a month and a half painting it and putting it together, and it's GREAT but still not perfect...even tho it's exactly how I ordered it, and I spent so much time setting it all up.
I payed about as much for the Gibson, and it played and sounded great as soon as I got it...and still does.
About Warmoth, and other parts guitars... they're a big money loser if you try to sell them whole. And you pretty much have to part them out to sell them on ebay, because Fender has people watching ebay, and they'll shut your auction down. I think the deal is that the peghead shapes are copyrighted, or something like that.