Crank angle sensor is fine.
It has a constant resistance and produces an AC voltage when cranked.
Rumor has it, as there is now no spark, it may be an EWS issue, although no fault codes (50% chance of getting one for the EWS, unless its dead).
The not priming is the issue that I cannot get any information on, although the FPC and pump work fine.
Turns out the EWS controls all the start procedures and if it gets moody, it plays with them.
Lets some work and not others, for a while, then disables more until the bike wont start.
Thats why it was fine when I got it going, as the EWS does almost nothing (may effect idle, hence the cut outs while warming) once its started.
The following link is the best description I've found so far.
Motorcycle Info Pages - R1200GS Electrical stuff > EWS Failures & Information
The BMW dealer I bought it from is doing a search to see if it has any outstanding re-calls, yep had to talk to them.
While looking closely at the bike, I've just noticed hairline cracks in the paint on the frame, above and below the telelever frame connection point.
No rust, so they are either fresh or not frame cracks.
One problem at a time please Mr BMW.