A bit of an update. After swapping over the ECU’s I then proceeded to ride the “faulty” bike for 4 days straight, commuting to work and doing all my normal riding. I consistently checked it after each ride by trying to start it back up after 5, 10, or 15mins and the bike never failed. I definitely would have had it fail to start previously within those 4 days if the problem was still present.
I then started riding my usual “good” bike which now had the “bad” ECU in it, and I was fully expecting to have that fail to start at some stage, but it seems it too is running perfectly and I can’t it to fail to start either!
At this point my working assumption is that the issue was ECU related but I fixed it when I performed the reset of the throttle sensor position and idle speed control valve. Aside from swapping the ECU’s between bikes, that’s the only other thing I did on both machines. I’m still riding the “good” bike and I haven’t tested it as much as I would like, but so far it doesn’t seem to have inherited the problem.
Finger crossed I've had a lucky solution. I can now put one of the bikes on the market, which will please my wife immensely!