I wanted to thank Zaga for his insight here as I had all sorts of trouble when I rewired a 2003 motor into a 2004 frame and converted the electrics to run all SEM system.
I could get a spark with the plug out (and I'd checked that fuel was there) but could not get the thing to even "cough' when the plug was in. Turns out the battery was just a little weak even with a small charger hooked to it.
This resulted in a slow crank rate with the plug in and the bike would refuse to start. I naturally thought I made some error in the re-wire. With the plug out of course the motor spun over much faster and spark was obvious.
I replaced the leads with ones that had larger surface area on the plug ends and hooked these to a car battery that was hooked to the charger and the bike fired up first go.
Another thing that I found really helped was to give the throttle 5-6 full revolutions to pump fuel in as my bike was on a work stand and had a temporary fuel bottle hooked up for my trial runs.
So thanks Zaga the comment regarding the critical RPM speed for spark backs up exactly what I found.
Regards
Anthony.