I may be able to help here, I have built and tested this kit but not yet installed it (S2BB dizzy working great for me right now, got other stuff to do). Be warned, this could get wordy
I totally understand your comment, but bear in mind the "instructions" are just copies of the Silicon Chip magazine articles this kit came from - written for electronics techies, all Jaycar have done is assemble the parts in one bag so you don't need to tediously order them separately and give you a copy of the article so you don't need to find a back issue. Would have been nice to include a plain English version though ! aaaanyway...
The diagram you uploaded isn't the one you need to follow unfortunately, the coil and magnetic pole-piece arrangement in the S2BB dizzy is actually a reluctor type. The S2BB module on the side uses the AC pulses generated by the reluctor coil (black wires, terminals 3&7 on the module diagram) to time the charge and discharge of the ignition coil via the green wire - this is the wire that would be the points connection on an old-school dizzy. The pink wire is just +12v to power the module's electronics when the ignition is on.
Seems to me you've got 2 options here -
Build version A of the kit (P68,top), leave the S2BB module intact and run the green wire to "Trigger Input from Points or Iginition Module". In this format it's working as an ignition interceptor, it's certainly the easiest option (less kit parts to change and no surgery required on the ignition module). The fact that you need the dizzy's ignition module to keep working isn't such an issue since it no longer has to sink big amps into the coil itself which is it's most likely failure point - the big 100R/5W resistor you need to add to the kit circuit board for this version acts as a load for the BB module but the current required is much lower.
Or, build version C (P69,top) using the 2 black wires you can see with the dizzy cap off (the reluctor connections). In this version you take the dizzy's ignition module out of the picture entirely, which may or may not help your clearance issues but will be one less thing to fail. The downside is more kit parts to change and some surgery on the dizzy module - I haven't opened mine up to look but if you could simply unsolder the green, pink and 2 black wires and neatly connect one black wire to pink, one to green with heatshrink on the connections that would be pretty neat and tidy and allow return to standard should the need arise. If that's not possible then however you do it the two connections at the reluctor coil under the cap need to end up connected to the "From Reluctor" terminals on the kit circuit board. If you have access to an analogue (scale and needle) multimeter put it on a low DC voltage range and clip the leads to the reluctor coil terminals, then turn the dizzy the way it turns when the motor is running and watch the needle. As the pole-pieces pass the pickup the needle will jump one way then the other very quickly - ideally you want it so that if the needle jumps in the positive direction first, the reluctor coil terminal you've clipped the negative lead to should end up connected to the round solder pad on the kit circuit board, the other one should be connected to the square solder pad (0v). This isn't crucial but will prevent any tiny timing errors across the rev range - the kit circuit looks for a -ve going pulse to trigger from so it's best if the reluctor coil output jumps in the negative direction first.
imho, I think if you're going to use a S2BB dizzy to do this leave the module alone, go the interceptor (version A). I can see no obvious technical advantage to version C, and version A is just as elegant, leaves the dizzy intact and I've just realised - gives you a limp-home option if the Jaycar kit fails
Just reconnect the green wire to the coil -ve instead of the wire from the little Jaycar "Trigger" module and drive home bearing in mind you have no mechanical or vacuum advance systems because you presumably locked them both out already. Crap, I built version F for my old Pirahna-optical dizzy and now I am seriously thinking I'm gonna break out the soldering iron and go for version A and the S2BB dizzy instead
Sorry about all the words, but thanks for getting me thinking about this - the Jaycar ignition just upped itself in the priority list.