Charger turning off and on near full charge is normal. Regen "pulsing" hot off a charge is also normal.
Let it balance (leave it plugged in for a couple hours after a full charge), then go ride, rinse and repeat.
Always listen to promotech.
Just another thought, I wonder if you managed to reset the BMS correctly? I've never done it, but your last comments around it being a software issue makes me think a reboot or the equivalent has to be worth a try. Resetting the BMS is the nearest I'm aware of. Your bike has been fine for years with the same software on it, after all.
One really long shot is that somehow the firmware has got corrupted. Again, a reset could help, but the act of getting the firmware update might just fix an issue that could have cropped up with the way the original firmware was stored. Memory of all types can fail. That really is pushing it a bit and is only a suggestion to run by a qualified person.
Another reason for suggesting a firmware upgrade is that it might cope better with certain parameters. You mentioned cell balance and your current firmware might be struggling with that a bit. New firmware might have some refinement that helps.
Do what promotech suggests first. Everything he says makes a lot of sense. He's one of the rockstars on this forum.