I've decided to build a custom electronics setup for my new guitar.

Here's a list of components.

Pickups: - 2 Seymour Duncan Humbuckers.

Pots: - "Classic" Fender Setup 1 Volume & 2 Tone Pots.
- Peak Expander Warm Tone Controller
- Tube Screamer Pot
- Distortion Pot

Switches:- 3-Way Pickup Selector
2-way kill switch.

Basically I want to install a normal fender setup with a 3 way pick up, and replace one of the tone pots with a peak expander.

Then instead of running it straight to the output jack. I want to run it to a secondary 3 way pickup. This one will not act as a true kill switch, but kill the tube screamer and distortion pots from the sound.

i.e something like this

Can anyone help with the wiring diagrams or see any difficulties I might face?
You'd need to use a DPDT switch for you "killswitch", which I will refer to as a bypass from here.
Why do you need both pedals/circuits? Will you have enough room in your guitar? Put a smaller overdrive circuit in there than the Tubscreamer, like the Stratoblaster from generlguitargadgets.com.
Anyway, you wire the bypass exactly as you would a normal pedal bypass, I'm fairly sure. Just place that circuit right before the output, as you have it in your crude drawing. I don't know much about adding pedals in the circuit, you may want to search the GBC, plenty of people have done it before.

I don't know that you can have two tones with a 3-way switch, if you don't have two volumes. You might have to go with one master volume.