Whats the best way to do this, modify the 21 loom or swap in the 18 loom and electrics?

I've gone the other way which is 21 engine in my MC18, the main difference is the gear position sensor on the 21 engine which will have a block connector, I expect you can locate the neutral wire in the 21 loom and wire it back to the 18 neutral switch, or just leave it disconnected if youre not fussed about neutral light. Other than that I guess it comes down to PGM choice, obviously if your talking about MK1 PGM like I have then your also into PV control units, which can be good or bad depending on how you look at it. Bad in that its 2 other electrical things to go wrong, but good in that the PV controller wont fry your PGM. 21 ignition timing is also more advanced on 21 so you may want to think about what pick ups/flywheel you use.

Ok thanks, i ended up going for keeping the 21 loom and electrics but im not totally sure what to do with the GPS wiring in regards to what will the PGM3 make of nothing being connected, what gear map will it default to? To me there seems no way of having separate 1st,2nd and 3rd maps and then 4th,5th and 6th wired to the 3rd gear map or is there?

No easy way to have the two maps, you're better off going conservative and splicing to the 6th gear.

I thought the reason you normally splice 4th,5th and 6th to the 3rd gear map is because the 6th gear map wont let the bike rev out as it should??? Surely id be better off splicing all gears to the 3rd gear map if thats the case?