SOunds like two seperate issues here.
Indicators.
The problem with your indicators sounds like a bad ground connection somwhere. This means that the voltage is taking a odd route back through to the battery.
The alternative is a short. Check the looms where they go throuh holes in the fairings, frame etc.
Trip.
This sounds like a battery backup issue. I suspect (check with Yamaha) that the clock have a perminant live connected from the battery in order to retain the trip meters and clock. My guess is that this has been broken ti the demoval of the alarm
The alternative is that the clocks have an internal battery (like a watch battery) which allows the memory to be retained. This may be low. Check with Yamaha, they will know.
Get a haynes book is my last bit of advice. That should tell you a lot.
