OK, an update. A couple of days ago, I was running the 50mm kit with 8.5 gram rollers. The scoot was running quite well, though the take off was rather lax once going it had a nice sort of pull right through the full range, top speed was about the same as previous, so no gain there from the 44mm crank. I did a bit of a check over, removed the flywheel to check all bolts were tight, retorqued head bolts, gained a 1/4 turn on each, saw no signs of leakage around head or base gaskets. As an experiment, I raised the carb needle 1 notch to the centre setting, test rode the scoot, it seemd a little off but thought I would see how it goes going to work and back. Being on afternoon shift I was hoping for an easier start at night (starting to get cool at night now). Going to work it was absolutely dismal, way too rich but struggled on and changed the needle setting back to where it was after work but, it was still as bad coming home. Pulled the jug off today and found there was leakage from the head gasket, but no other problems. As a trial I raised the cylinder approximately 1.5mm, this gave me exhaust port duration of 192 degrees and transfer port duration of 148 degrees.
From memory my port durations were ex. 188 and trans. 130 degrees. It is now running very poorly, struggling to make 60kmh.
I will have to go back and read Gordon Jennings' handbook again and try to work out what I should do with the port timings. I would now like to trim and fit the new kit, but I don't want to do that while I have an underlying problem.