Spent some time reading this thread and am inclined to think that the VR is shot.
Symptoms of course only show up when it gets hot. VR's are what's called shunt regulators... ie when the battery is charged they shunt the current to ground which causes heat.
If the voltages are all over the place that suggests fouled connectors. The AC your seeing sounds within spec.
With the ADV bikes the regulator is in a place that is very susceptible to water ingress, as well as the battery. If the battery has connectors similar to a motobat battery make sure that the posts are on tight and that the earth strap has been removed and cleaned.
One would also think that and 8ah battery would be way too small for a 990.
The 12ah battery on my SE will run UHF radio, Heated Grips, two Lightforce Lights & Two fans with very little voltage drop.