Regarding water in the R65 fuel tanks...
With only a single petcock, it's not possible to be assured that any H2O in the tank is completely drained when using the petcock while the tank is mounted. There is always some residual fuel -and possibly water- in the right side of the tank. That "hidden fuel reserve" can hold water, too.
Best option is to remove the tank and drain it completely. It's not necessary to attempt draining through the filler as the flange inside the filler neck prevents a complete drain. Just be sure to slosh the right side over to the left and -for best results- remove the petcock during the drain process.
BTW, that hidden fuel reserve can get you a few extra miles even when you've run the "reserve" dry. As you are already parked on the side of the road, tilt the bike and splash that last bit of dino fuel over to the left side. Hopefully, there won't be any water in the gas.
Water in your gearbox is often a result of a worn and cracked rubber speedo cable boot located where the cable enters the box. Replace the boot with a new one and pack the inside of the boot with grease just prior to snapping the boot onto the box.