You cannot run with the battery disconnected - The R/R requires to be connected to the battery to give an output.
The bike dieing is the correct repsonse. Nothing wrong there.

I'm actually surprised it idled at all - typically shuts off immediately

If all three phases are equal voltage and it is NOT short to engine case, then there is no problem with the stator.

Revisit the R/R again
You can even check your original first
Need to measure between each of the three input (stator) terminals, to each of the output (+ & -) terminals.
None of these should be short.

Last edited by DEcosse; 07/01/2011 2:00 PM.