I agree with 1971DT250 said.  Something isn't right with the ignition parts.  My thought was when it was said the points were "almost new", something was wrong with the new points?  I'm kind of biased as I've seen several point magneto ignition problems caused by "new parts"...   I've actually fixed a couple of them by re-installing the original points and condenser...  or new OEM quality parts.  

One thing I want to point out is that timing in degrees BTDC was never "double".

2.9mm BTDC is about 20.9 degrees BTDC.  Double that to 5.4 mm BTDC and you're only at 28.8 degrees BTDC...  only about 8 degrees advanced.  Due to con rod angle geometry, piston movement is not linear near TDC.  

I'm a page behind but I'll catch up. An advance stator can't be used with a non adv flywheel, the cam won't reach the points.
 as they sit further out on the plate due to the fat cam. Must be fitted as a pair. Be unlikely yamaha would have a different left crank half for adv & non adv with keyway moved a few degrees. I've mix n match cranks without contemplating that, or maybe I just struck it lucky but not feeling lucky these days. My RT1 cylinder had the decomp plus advancer & could damage near start it by hand if you were brave enough. Mind you it was worn out with low comp but still ran good around the farm. Almost trials bike with the valve open. Poor old thing.