Ahhh there is the kicker. Once I get to the 2000 grit or so, I have to use metal/aluminum polish to get the chrome like shine to pull through. Its just varying degrees of rouge down to the white rouge which is about as rough as car wax. This process puts all kinds of oils into the aluminum that clearcoat will not adhere to. So I'm in the same boat. Every once in a while you gotta get busy with the polish and toothbrush.
I've tried a few different finishes that allowed me to clearcoat, but I was never impressed with them. Most never rivaled the factory level of luster. So once you rip off the factory clearcoat and polish the aluminum with the rouges, you're doing it forever baby. Well as far as I know anyway. I've heard rumours of a new generation clear, but have yet to see it - or use it for that matter.
Also, do I understand that you essentially tore down the whole engine and polished/sanded each piece in it's disassembled state? Unbelieveable.
Ummm yeah. A real labour of love. The engine came apart and each piece was done by hand. I tried for one piece a night, but the cam cover and tranny cover were real bears and took several nights each.
Here's a shot of when it was going back together. The sub-tranny cover is still off. Why? My knuckles needed a few days rest at that point.

Also, how do you like the 10 speed tranny on the 900? I met a guy that used to have a CB1000, which I believe has the same tranny. He told me 99 percent of the time, he used the lower ratio range, and simply shifted to the high range for interstate highway runs. Almost seems like it would be better to just have a 6 speed box with a real short OD for 6th gear. Just curious.
Pure Honda marketing. At that time only the Gold Wing GL and CX/CT500 had the right hand shaft drive. Honda knew there was a market for a large displacement (for those days) inline air cooled 4. It could double as a basic bike, and then be loaded with a fairing, saddlebags and such and be a tourer. However to use the GL's and CT's rear drive the had to get the power from the left hand chain to the shaft driven right side. Cheap and easy - toss on a sub-tranny and call it a 10 speed. Its really just a dual ratio rear like on a 5 or 10 ton truck. And yes, use low around town, and put in high on the highway. Not really a tranny as such.