Hi Trevor,
If the engine is stopping suddenly enough to work the flywheels loose then i guess something is wrong internally, personally i would strip the engine and have a look. I think the crankcases split horizontally on the M91? If so try to remove the crank, bearings and flywheels as one unit, this may make it easier to remove the flywheels. You could try a hot air paintstripper gun to warm the flywheel centre and try to twist it off, some penetrating oil helps here too, but be careful not to twist or bend the crankshaft.
The main bearings are needle roller type and so have no sideways control, on the M90 the shell of the needle bearing acts against the crankweb to limit endfloat (bearings are positioned in the crankcase to allow clearance but little side to side play on assembly). As there is little sideways thrust this design is sufficiant. To check the health of the bearing, once you have it apart, just look for scores on the crank where the bearing runs and check the needles are running in the shell freely, not twisted and evenly spaced. They are normally a sloppy fit on the crank so some radial movement can be felt, this is by design. Normally needle bearings are very reliable and require minimal lubrication, but if they have run totally dry the cage may break up allowing the needles to twist and pinch the crank which may possibly be the root of your issues though i would not bet a weeks wages on that being the case :-)
If you need and pictures of how the parts 'should' look just give me a shout.
Hope this helps
Ade