Late to the game but a couple of comments:
Where in the FSM does it say anything about applying GREASE to the PIN? Its not needed and will only attract debris. I would forgo this action! If the pads don't float as required its because the pistons are NOT retracting.
Bleed the brakes. If that does not solve the issue, the calipers should come apart for cleaning and inspection - replacement of the piston seals.
DOT 4 FLUID: is hygroscopic, it attracts and retains moisture. Its replacement interval on a motorcycle should be YEARLY!!! IF YOU OPEN THE BLEEDER for ANY REASON. Replace the fluid and BLEED THE BRAKES!!!
I highly recommend a turkey baster or a syringe to suck the old fluid from the MC. This will reduce the time required to flush the system and ensure that new fluid is the only fluid in the system.
Lastly: If pads are NOT OEM pads, confirm the total thickness is not the root cause.
Backing: 3.99mm
Rattle Clip: 0.40mm
Brake material: 4.49mm
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Total thickness: 8.88mm
If the pads are thicker than OEM for some reason, it "could" bottom the pistons in either side of caliper and cause excessive drag.
FWIW - I just measured some new pads.. .. .. 5VN-W0045-00, Genuine Yamaha
definitely a must wish i thought of that, could be chasing your tail with too thick of pads. but after that it check the piston movement.