My Keos came with overhaul instructions -- seems pretty easy. Do you have the instructions? I think you use a pretty common wrench size and remove the spindle, then clean and regrease the needle bearing. (The other bearings are cartridge models and should be fine.) Probably your LBS can do it for you.
Your Ultegra BB should be fine unless you ride lots in the rain and such.
You sure it's not the BB? Tried swapping out pedals? I might do that before I went to the trouble of repacking the pedals. I had this noise and re-installed my BB three times before I got it to go away. Teflon tape was the only cure.