lights flickered and then bike died

[BBS360]

Yeah, the grounds would be redundant on combo units.
Without knowing more about it I couldn't say for sure what the problem is, might be impossible to say without trying it.

It's the wiring at the alternator connector that needs the change for the later model electronic regulator to work. Everything at the reg/rec should be fine as long as it matches the stock connectors.
Off the top of my head there should be a blue, yellow, black, and green wire coming from the alternator (blue and yellow for oil pressure and neutral switches). The green would stay as-is but the black needs to be rerouted from ground to battery voltage, preferably directly after the ignition switch.
I know there is a thread where someone makes the change. I'd have to look for it tomorrow.

It would of course need to be changed back if you ever wanted to revert to the mechanical regulator.

 

[NewHavenMike]

I may have come across the thread already. You posted in it as well. In that thread, you mention you have a cbr125 regulator?

Id like to know exactly how you have yours set up and if its been working out for you. I also have an AGM battery. Someone should make a tech post about this. I EBayed another mechanical regulator today because it was cheap. This should hold me over for a while. I really would like to get a more up to date system working here so I can clean up the wiring and get it all finalized.

 

[BBS360]

The CBR125 regulator plugged straight into the stock rectifier connector. By random luck I had a source for a free one and it just happened to fit.
Same connector and I'm pretty sure all the wires were in the right spots.
The hardest part was mounting it near the stock location so it wouldn't interfere with the rear fender. Had to bolt it to a short piece of metal to offset it forward on the battery box.

Currently running a Transpo IB301A adjustable regulator.
https://store.alternatorparts.com/ib301a---voltage-regulator.aspx
It's the correct type for the XS360. Needs connectors done up to plug in but no rewiring at the field coil.
There is a non-adjustable version, the IB301.

It all tests great with the bike on the center stand. Voltage in the usual (low) range at idle, increases with revs to 14.5V and doesn't go any higher.
With the stock setup it would get up as high as 15.5 or even 16V.

That being said, I am chasing some performance issues. I believe they are carb related but this thread has had me thinking about it again and a loss of voltage could explain the issue.
I'll try to get a voltmeter installed where I can see it or somehow get my Bluetooth meter to log voltage as I ride.

The IB301A has been used by quite a few people on other bikes and vehicles.
Should be a good choice, though there's also the Chrysler style here:
http://www.xs400.com/threads/aftermarket-regulator-wiring.7479/