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So the last two oil changes have been Shell Rotella T as opposed to ATF type f. Probably not related but anyway. The last two changes have been a little milky. I assume this means I have a leaky water pump shaft seal? I have not lost enough water to be able to tell.

Is that seal in the outer case? Figured I would change when installing revloc and clutch actuator seal.

I have a manual...

yes, you might have a leak at the water pump seal. that is call a mechanical seal if i am not wrong. it comes as a complete set that has a spring kind of seal. check also the bottom of the water pump if any coolant leak from the litte hole below.

rotella has always come out a little milky looking in all the bikes i've used it in

if it's milky as in milkshake, yes, the seal around the water pump impeller has failed. Very common. Make sure you replace the bearing it rides on while you're in there, and check the shaft for wear where it contacts the seal.