Well...
Everything except the tacho and number 4 cylinder, which isn't getting as hot as the others. I've added my stick coils to the bike, and will have to investigate why. The bike 'sounds' fine and doesn't sound like it is dragging a cylinder. I'm guessing it is either the connector on the coil, or the plug, or the fact the bike was started from a completely 'dry' state and it took a while for all the cylinders to chime in (it was also 10.30 at night and I didn't want to run the bike for long as I have enough issues with my retarded neighbours already). I'll investigate that tonight. There are only limited causes for one cylinder doing that as the coils are in series as pairs. Easy fix.
The tacho is because my battery health indicator is wired into the loop, the indicator is a polar module and I have no doubt put it in the wrong way round. Easy fix.
I now have a wiring loom that has no unnecessary plugs, just enough length to reach from one end of the bike to the other, can run either the HRC or stock CDI, can be converted from charging circuit to no charging circuit, and routes tidily from one end of the bike to the other.
Job done.
