As some may remember way back I did some charging testing and found charging the battery on the bike, a clicking noise would occur as battery was almost fully charged. It would click more rapidly with the LI battery and seemed to be cycling a relay and priming the fuel. I had been using the old standard Battery Tender jr. Nobody seemed to be forthcoming with a reason or answer as to why since 2013, so I advised to always remove the battery to charge for safety reasons. View: https://youtu.be/DYS1RBrnDE4 Recently decided to get a second unit to charge a few vehicles in the garage including those with LI batteries. The Battery Junior 800 has ability to switch between lead acid and LI (manual button you switch before connecting to bike) and while supposedly not for sale in CA, I bought from Amazon. I am sitting in my garage with the bike hooked up and battery reading fully charged and no clicking noises at all. I would still only charge on the bike when you can monitor it but the Battery Tender Junior 800 appears a good buy.
Are you very sure the clicking and the whine wasn't coming from the battery charger ? Because most smart chargers do that ...
Clicking was the bike. It also flooded my bike. I think the old BT Junior caused a spike like the stator would so triggered the fuel relay. The new BT Junior 800 seems to have better circuitry. I am no electrical guru so just my thoughts. I found this early on in '13 and a couple of threads about it... http://www.cafehusky.com/threads/battery-charging-14-te-310.80108/#post-529158