Cool, i like the look of that Strat. Some good ideas too.
I started a similar project earlier this year...

For the custom pickguard i drew a template up half Strat/half Jazzy and Augustus McCrae (on these boards) made me one. However, to make the Strat dual circuit i think you will end up routing even if you do not use the top horn style controls. Bob is right, you can set the plunge depth on the router so dont worry about busting through the other side. Just take your time setting it up and remember to take into consideration the body is thinner where the contours are.
You may cram them all in by the use of mini switch's or maybe concentric pots, i'm not sure as my electronic knowledge is limited. There are users on here that could tell you how to but they rarely visit these days.
If you do use dual circuit you will just need to fit the extra tone and volume controls and a master two-way switch to go from one circuit to the other. I have'nt got round to putting the second circuit in yet partly to loosing interest and not being able to find a supplier for roller pot brackets. So at the moment the two-way switch just acts as a 'killswitch'.
Definitely keep us updated.