Basically you are on your own and can decide what you want to do in Kyoto. You can also take a train from Osaka to Kyoto yourself without joining a tour.
6:20pm should be ok. It takes about an hour to go through Custom and Immigration. An hour to get cash and tickets. Just do some research as where all the counters are located. The Limo bus ticket counter is near the exit to the buses. Suica cards can be purchased downstairs. Have one person watch the luggage so it will be easier.