Good news! after messing about turning the ignition on and off while riding the bike, and the problem temporarily going away, I decided to remove the fuel pump and inspect it again. Before I removed it I did a flow test and got the usual 300ml with three cycles of the ignition. No change there. I removed the pump, disassembled and very carefully reassembled. The only thing I did differently was I mated the pump motor with the top high pressure fuel filter before I put the mated the bottom housing and inlet filter. It felt like it had a nice tight seal with the o ring on the pump motor outlet and high pressure fuel filter top. I refitted the pump and to my amazement all the issues have gone away. I rode it with a fairly low fuel level, two bars on the gauge and no issues, then filled it up and again all good. The bikes performance has improved dramatically now, much much faster and no flat spots anywhere. All I can think is that while the pump had good fuel flow it didn’t have good pressure and was bleeding off pressure somewhere from one of the o rings in the fuel pump housings. Maybe I pinched an o ring last time I assembled? Although its a bit of a mystery I am stoked that its finally fixed. I rode it today for 100kms and no issues at all.
On a side note, next time I ever have to work on a motorcycle fuel injection system I am going to buy a fuel pressure gauge. I think if I had one of those to start with I would have saved myself a lot of time.