The loom looks fine to me. I do keep getting the fuel gauge flashing constantly since I put the power commander on, checked all the connections to it this afternoon and they seem fine. The underlying problem started way before the commander was added though.
I'm thinking of taking the bike bike to standard and going from there, at least it will eliminate the pipes, filters and PC from the equation. I've bought a new NGK plug cap and plug, just need a decent HT lead (any recommendations?). My plan is to ride the bike until it starts to happen, change the plug, cap and lead at the roadside and see if it helps. Cold and damp weather seems to increase the problem, I think it has to be electrical. Is it ok to put a bit of silicone grease in electrical connections to help keep damp out?

Thanks for your help Kev, this is really starting to get me down now!