could be one of several issues, or a combination of things.
Engine dying problem means something is draging the clutch bell. Usually its cause by broken clutch springs, or a hung up shoe. but you also need to check a few other things if you still have problems. Are the clutch shoe pins in the flywheel loose or bent? Do they stick out more than 1mm farther than the clutch shoe? Is it the wrong clutch bell? Some have a large champher inside, and if the shoes are riding on the champhered part it puts a lot of forward force on the bell, uneven shoe wear, overheated bearings and clutch parts, etc, etc.... You said you shim the bell with no end play. Well there should be just a little end play in it when cold. Have a good look at your clutch nut and flywheel as well. You may see signs of rubbing or stange wear marks that could point you in the right direction.
Gear mesh could be a issue. Chassis flex can cause the mesh to change drasticly when running. Check the stiffeners. Check that the moror mount is not cracked or loose. Also check your gear alignment.
chances are that if you fix the clutch draging issue, your bearing problems will get better. On the bearings, do you oil them or run them as is? Oil works better than factory grease most of the time. You still need to inspect, clean and re-oil, or replace them after about every 10 tanks. Ceramics might hold up better, but I'm not really sure if it's worth the extra cost.