Ok finally sorted the ignition problem, was not the ignition switch, was not the connector under the tank, that i've now fooked, well not true the ignition wire has been bypassed. The problem was.... drum roll.....
There is a black wire coming off the + battery terminal main wire, this goes through a connector and turns to a brown wire the otherside. This cable feeds the rectifier/regulator. On close inspection the connector had gone green and powdery and did infact crumble to bits in my hand. I took out the offending connector and replaced it. Hey presto, after giving the bike a good run, it now runs fine, apart from i now seemed to have developed the high idle problem, its not all the time and settles if you pull in the clutch, so not sure if stepper is on its way out or the TPS is, or if its a residual left from the connector problem.
The thing i found hard to fathom with the ignition problem was the fact that when i left the bike a while it would then start and run fine for a few miles. But now i know it was this connector its clear that, the cable was heating up and causing to much resistance in it, not uping the amps so the fuse would blow, just uping the resistance.. So one to look out for if you get similar problems. The connector is under the R/H sidepanel.