A couple of kicks, IT STARTS!!. Stop engine and check everything again. It starts again, it won't idle but I'll fix that later.
Get bike out of garage, start, engage first gear and off. Beautiful it feels smooth, engage second gear, off we go, smooth and pulls ok.
Engage third gear, didn't engage, try again, NO THIRD GEAR. Back into second and back to the garage. Trouble finding neutral, but get it eventually. Examination shows that the gear lever has lost spring and won't spring back to the original position. I go through the gearbox carefully while the bike is on the centre stand. All the gears are there but because the gear lever isn't returning to the home position they are difficult to engage.
Good News - The gearbox is probably ok.
BAD NEWS - I have to pull the engine out again to see what I have done wrong when reassembling it.