One thought which caught me out a while ago. Did you by any chance replace the red multiway connector that sits under the seat? If so make sure the one you used is not the type fitted to ETZs. These have some of the connectors cross connected whereas the red ones are all separate. Created all sorts of odd electrical behaviour on my bike.
Your indicator problem is almost certainly poor connections inside the winker units or poor earth connections. Winkers take 6amps so doesn’t need much to drag the voltage down
Have you tried using a voltmeter to make sure the system is charging properly even under load? Having the warning light go out is no guarantee of a fully functional system.