Try Busch Suoer Shine Aluminum Polish and follow up with Busch Aluminum Wax and Sealer. A friend of mine recently gave a bottle of each and I have found it to work very well. Not sure where to get it though.

 

Stick with the simple stuff. Foamy Engine Brite and cans of spray brake parts cleaner. Every home shop/garage needs a few cans of each.

 

I would imagine that the clear coat that HD used on the covers, has yellowed, and is beyond help. Or, in the case of my 93 FLHS (which had the aluminum cases and polished covers), the clear coat has chipped off along the leading edges, allowing moisture to creep in and discolor the aluminum.

You're faced with a couple options, depending on how much work or money you want to spend.

 

Hackd......haha, this is funny. We're both on Jeep website (i recognized your picture right away). I'm Military Jeeper on all the Jeep forums.

Thanks for the gouge above as well.....

 

I've found aluminum not only to be the softest metal around, but the easiest to work. Say you have a lacquer coating on the cases that has yellowed. No problem save for elbows. You SAND off the coating with about a 440grit wet/dry paper using water (always) leaving the cases look like satin in a way. Then you go through the grits all the way to 1500, which will start to show your reflection pretty well. Next you get a paper grocery sack, and avoiding the glue seams, sand it with that. That's 2000 grit.
Next, your aluminum or even auto paint POLISH, (not wax) and a microfibre cloth will make it look as good or better than your chrome. Then wax, and you're done.
If you skip grits in the sanding, you may end up with swirls; this is one disadvantage.
This is actually a heckova lot of fun watching it develop.
BTW, while doing this, do it to your auto headlights that are fading, using just the paper bag and polish. You usually don't need to buy a kit.