Thanks d8veh, I think all is ok now. I'll put this post up in case it helps anyone else.
I checked the hall sensor connector and although it feels like a loose fit (or at least slides in very easily) I'm satisfied that it's making good contact. When connected to the tester all the hall indicators light up in turn and when connected to the throttle the wheel turns.
I was ready to replace the hall sensors thinking the sync problem must be to do with their position. It was a bit of a bodge when I put them in. I thought the best method would be to put the epoxy in all three positions and thread the hall sensors through the holes on the pcb so there's not a problem lining them up once glued in. The epoxy obscured the gaps where the sensors were going into and trying to line up all 3 got a bit messy and I think one of them got pushed down further than the other 2. My advice to any fellow newbie doing this for the first time would be to glue each sensor in separately before putting the pcb on.
So I took the motor out again. There was something else that had been bothering me in that there was a gap on the shaft between the circlip and the clutch/gears after I'd put them back on (I took the shaft out when replacing the phase wires). I had another look at this and decided that the gears were rubbing on the back of the magnet bowl that contains the stator. I decided this was the cause of the change in motor sound and needed fixing so levered it back up the shaft. This requires quite a bit of force on my motor, compared to the description by spinningmagnets on his MAC tear down thread on Endless-sphere. So having shifted it up a bit I decided to put it all back together and test it. I was really reluctant to start chipping out those hall sensors again!
Anyway I took the bike out for a test ride and got the same judder at half throttle. I took it up the hill where I got the clutch slipping feeling on the 2 previous road tests and that had gone. The motor also had the same higher pitched sound as it used to.
I suspect the difference in relative position of the hall sensors is the cause of the juddering (sync issue) at half throttle. But since this only lasts for a couple of seconds as accelerate through this speed I feel I can live with it. Please let me know if this is likely to damage the motor or controller.
Thanks again d8veh for all your guidance.
I'll just add one other thing for anyone reading through this. The wires passing through the shaft on the MAC motor are VERY tight. I tried pulling them through but it wasn't gonna happen so ended up cutting and replacing. The protective sheaf around the old wires didn't even budge once I'd pulled the wires out from the controller end so there is no way it would have pulled through round the 90 degree bend at the stator end. Spinningmagnets makes this point in his tear down thread
http://endless-sphere.com/forums/viewtopic.php?f=16&t=51310 - trying to pull them through just tears the insulation off. In my case levering with the pliers also scratched the stator windings, fortunately not deep enough to cause a short and I've painted some electrical varnish on the scratches to be sure. It at least gave me a wake up call to be careful on how I handle the stator!
