Well I spoke to Jason at Baja yesterday and he was very helpful, here's most of the questions answered...
1. Is a TTR230-specific install guide available? A) Yes, I was sent the wrong one
2. Once the kit is fitted, does the bike still keep the old ignition power switch/button? A) Yes, the old button remains, the key switch acts as main power for the lights and replaces the kill switch - it kills the engine in the off position
3. Where do I fit the switch for the brake pedal? A) It's described in the TTR230 install guide with a picture.
4. It looks like it makes sense to drill a hole through the rear mud guard to allow the rear tail light and turn signal wires to come through - where is the best location to drill the hole? A) No hole needed, the wires thread through past the rubber grommet that is around the frame tubes that poke through the rear mud guard.
5. Baja (with my consent) shipped the kit to me without the front brake pressure switch which was out of stock and is coming later, where is that fitted and how does it connect to the wiring harness? A) It's an optional extra that comes with a wire that feeds back to parallel with the rear brake switch.
6. Kill connection. It looks like there's a 2-pin plug inside the headlamp assembly that has a pre-wired kill switch connector that plugs into the connector that I unplugged the old kill switch from - is this correct? A) Yes, the TTR230 kit comes with a pre-wired plug that goes right into the connector that you remove the old kill switch from.
7. Headlamp relay orange wire. The TTR125 instructions talk about splicing an orange wire (that's not in my kit) to the yellow wire on the regulator and routing this to the orange wire on the headlamp relay which seems not to be in my kit. I'm thinking that this is only needed for non-battery applications - am I right? A) This wire does not exist in the TTR230 install, the only place the TTR230 dual kit 'touches' the existing electrics is by replacing the kill switch.
8. Neutral light. This is an idea I have that means I can have a green LED that lights when in neutral, I believe I can make it work by breaking into the neutral switch circuit and adding a diode, resistor, and green LED - if anyone is interested in this, I can create a simple diagram. A) I will try this and see if it works, then do a write up.