I just had a go.
Do you think the graph tech is a better way to go than the LSR nut that you find on deluxe strats?
Warmouth would be cool. I'd go with a simple oil finished (satin finish?) mahogany body and maple neck, and like you say, universal route, or even just HSH. I know nothing about trems. Is the wilkinson better in some way than the american standard?
Regarding Wilkinson, they are millions of times better than the Vintage or Original Trems. Just read reviews over the net. They are really smooth and hold tuning well. They hold as good as a floyd with locking tuners and a good nut (which I'll get too shortly). You can also get it recessed so you can pull up like a floyd, or just have it laid on the body. Hipshot and Wilkinson are my 2 favourite non-locking trems.
Regarding the nut, I've tried loads, and whilst the LSR works, the Graph Tech Black Tusq XL provides the smoothest, friction-free, string glide, for me personally.
On mahogany, I think an oil finish may work better. I think satin works better on harder woods like maple. I'm sure Feline or someone could give you better advice than me on this subject :)
With the neck, if you get maple, get quatersawn. But seriously consider raw Pau Ferro as the neck wood, andmaybe even the finger board. You don't have to finish this wood, and it has a lifetime guarantee. It's my favourite neck wood, similar sounding to maple. And it feels the fastest neck I've ever played.
But if you don't like the brown cosmetics of Pau Ferro, check out Canary or Afra. They're the tiniest bit warmer than maple, but no where near enough to really notice a major difference. There's descriptions on the Warmoth site. I mentioned these as they're similar in colour to maple, and they also can be played raw with a lifetime guarantee.
Just a few closing comments. As well as having fun designing your own Body & Necks (check the neck bit out if you haven't), check out the Browse & Buy section; it has really good savings. Also have a look at the Soloist too :)
