Hey there guys, just thought I'd give you a little update, even though the project isn't going to get underway for another few months.
I spoke to Tim today (to order a purple VHII with double screw poles, but that's a different story! :) ). He suggested something like a Crawler for the bridge humbucker, since it will be great for rock tones, then when split it will be very similar to a single-coil in output. For the single coils, he suggested Trilogy Suites, or Irish Tours if I wanted a more vintage sound.
The Crawler/Irish Tour set sounded perfect from the way Tim described it, but I'll definitely be trying out the BK'd guitars at the LGS to make up my mind though.
I messed around with the Kisekae builder and here was the result:

The colour looks very garish here, I'm thinking either a baby blue or mint green, but I can't be bothered to go through the whole designing process again. Also, I don't know which way round I want the toggle switch and volume knob to go.
Materials-wise, I'm still thinking of a chambered Mahogany body, with a flamed Maple neck and Pau Ferro fingerboard. That said, I'm also thinking about Swamp Ash for the body and Ziricote for the fingerboard. Still, it's early days yet.
Oh, and the unbuilt guitar already has a name - Lydia. Aside from the fact that I like the name, it also happens to be a track from Andy Timmons' latest album. Seems appropriate since it's his tone that made me want to get a fatter-sounding strat.
Thanks again to everyone who has taken the time to give their opinions so far, it's been much appreciated!
Nolly