Been out and about the last few days bedding things in after the rebuild... one thing I noticed was its slow to turn over when you start it. I had upgraded the cables, and the starter itself was good, so I had another look at the timing. When I did the map, I had the first RPM point at 400 with 10 degrees BTDC and the second at 1000 again with 10 degrees... so i changed this to 5 degrees from 400 to 1000, so there is not so much advance at cranking speed.
I also configured the software so it did two full dead revolutions before it sparks... this means the engine is properly spinning before it fires... It really spins over now and starts MUCH better