Yes, you need to remove the clear coat or you're just polishing it, lol. Any sort of paint stripper usually does the trick but some do work better than others. Then, you may need to do a little sanding to remove any corrosion. Fine (blue) and super fine (gray) Roloc discs work well for this too. Then finally, you can polish. A buffing wheel with a coarse compound will remove fine sanding marks (I sand down to 400 paper then buff). Then you can progress to finer buffing compounds but I usually don't go much beyond the coarse (black emery) compound. I'm happy with the shine that gives me, not show chrome quality but nice enough. Then through basic maintenance, every hand polish makes it look better.
Yes, all the polished aluminum parts on the later models were clear coated (fork legs, rims, side and valve covers, rear drum brake plate).