ENGINE DIES IMMEDIATELY WHEN BATTERY IS DISCONNECTED

I am experiencing charging issues with my 1981 XJ650. Battery is new and kept on a 2amp maintainer while bike is sitting. From sitting on the maintainer the engine will start right up and stay running. If I go out on the road and shut the engine off (e.g. to stop for gas) it will not start until after much cranking. I've been riding this bike for about seven years now and this is a brand new problem. I ran through all the electrical diagnostics in a Haynes manual and everything seems to be within spec. I removed the alternator brushes and measured them. Brushes are both well within spec. Someone told me to disconnect the battery while the engine is running. Their rationale is that the engine will run off the alternator alone; therefore, if the battery is disconnected while running and the engine dies then the alternator is at fault. Well I did this and the engine died immediately. I repeated the test several times and each time the engine died. Is this evidence that the alternator (either rotor or stator) is shot? Or am I missing something.

 

You're missing something.

And quit disconnecting the battery with the engine running before you cook your rec/reg if you haven't already.

BELOW 2500 rpm or so, the alternator does NOTHING. The battery is what runs the motor. If you disconnect the battery at idle the motor WILL die. The charging system doesn't "come online" until around 2200rpm, and should reach full output at 2500rpm.

Not starting until "after much cranking" doesn't sound battery or charging related. If the battery was low it wouldn't start, just crank and crank.

Sounds to me like you need to have a look at your valve clearances. "Starts fine cold but hard to start when warm" is a classic symptom of too-tight valves.