Maz wrote:
You would need to change the wiring harness and ECM because the 09 motor has a crank angle sensor, your 06 has a cam position sensor.
Maz, thank you. This is what I hoped for, your expert knowledge that tells me I'm being foolish. I may be able to get the harness & ECU, but it's not definite and it would mean pulling apart more of the bike to replace more bits, and I'd end up more out of my depth.
So, moving on then, I need to source parts, or someone who can/is willing to undertake a top end rebuild for me

(obviously for suitable recompense).
I'll get some pictures posted up in a few days to show the problem, but basically, as far as I can tell, I need a new barrel, piston, and valve set on the rear pot. But then, what's to say the other pot won't suffer the same fate later on? If so, now I've got the engine out on the bench, would I be crazy not to do a precautionary rebuild on that one as well - at the very least new valves/valve springs?
Nutah and others thanks for your inputs as well.