I don't know who told you that clear coat won't stick to polished aluminum but I don't think they know what they're talking about. The aluminum on my '76 H-D Superglide was polished and clear-coated when it left the factory new. Over time the clear coat will yellow and get chipped by rocks and whatnot on a motorcycle and can look pretty crappy. That's the way mine looked after 20 years so I polished all the aluminum on it, lower fork legs, primary and timer covers, and rocker boxes. The best way to polish aluminum is on a buffing wheel using polishing compound. I bought a kit of compound at Sears that ranged from black (emery) which works better than 400 grit paper because the paper loads up quickly, to red jewler's rouge. Brown tripoli followed with white tripoli is about all you'll need actually to make the valve cover look almost like chrome. A spiral sewn flannel buff (wheel) works best with these. I'd forget the clear coat if I was doing it and every now and then polish it on the motor with a good aluminum poilish like Mother's or SimiChrome which is the best I've used. That will keep it nice. If you want to do it right, you should remove the cover from the motor and I seriously doubt you'll finish it in one evening if you want a really nice job.
Even though I've polished a lot of aluminum, I've never done the valve cover on my FJ40. I figure no one sees it but me so why waste the time? It's not like looking a motor parts on a Harley.
HTH
Pete