Hi,
leaving Tokyo early and stop by Tokyo on the way to Osaka...
I presume you mean Kyoto....?
Schedules can be found on Hyperdia.
The earliest departure is listed as 6:34 AM. But schedules could change and you don't give any date.
As for having enough time, it is entirely up to what you have planned. Osaka is actually better from the evening to see Dotonbori and some other places. For the Kyoto places you mention, it should not take long. For Kinkakuji. you can be through it in 30-45 minutes tops. There just isn't much there aside from walking around the Golden Pavilion itself - nevertheless it is breathtakingly beautiful. For the Kyoto Imperial Palace you must make reservations first to go on the tour, which lasts 60 minutes or so. I did it in April last year when they opened it up briefly to seeing it without the led-by-the-nose tour. It is nice but honestly not overly impressive. You cannot enter any of the buildings. Instead I would suggest you go see Shugakuin Villa instead - there is a lot more beauty. It also requires advance reservations for its 80 minute tour, but it is free and you might like it more. Nijo Castle is also much nicer, and while crowded with a lot of tourists and a more draconian "no pictures" policy inside its buildings, it is well worth visiting.
As far as a tour goes, I'd say it's better to do it yourself - arrange what you want to see, leave out what you don't, and make your own custom plan that you are happy with.
Try looking through these guides to see what you'd like:
http://www.kyoto.travel/
http://www.ar.jal.com/world/en/guidetojapan/city_information/uky/see/central/