Agreed, no clear coat on red (or at least my red 899 didn't have it). When I've polished by hand my applicator was definitely red afterwards.
If you want to "fix" that, you can clay, then buff/polish by hand and apply a ceramic coating. After curing, simple 2 bucket wash method will keep the paint looking good for a long time.
Also, its worth noting that even brand new fairings come with a significant amount of marring and swirls from the factory. I had a fairing replaced and my new one looked worse than the old one with 12k miles on it.
For wheels you will want to stay away from doing anything that will inadvertently get on the rubber. Definitely no wheel/tire shine. If you decide to use a degreaser, kerosene, or WD40 for cleaning (all of which work fairly well)... then you'll want to apply it to a rag first, then wipe down the wheel. Rinse well afterward.