1. 3600 is recommended by the mfg, so no it is not too fast. You should just use light pressure and keep the blade moving. A slower turning machine is better, but what you have is ok as long as you learn the limits of it. I have a 3600 rpm buffer that I use, and have had no problems.
2.You should get a somewhat polished edge if you are using enough of the white rouge on the slotted wheel. Add some each time you strop a knife on it. Yes you should use the same angle on both wheels as close as you can.
3. If the "patches" are wax, and not bare paper, then there is enough grit on the wheel, as long as they still grind your knife blades. You should only have to re grit after sharpening lots (as in 100 or more) knives if you are using light even pressure. Let the wheel do the work. Mine show little grit and mostly wax patches, but still sharpen my knives ok. The wax is to help keep the blade cool when grinding.
It does take some practice to get it all down and working right. The key, I think is to use light pressure and keep the blade moving on both wheels. Sounds like you are close if your santoku will cut paper like you said. Get some old knives to practice on, or as Richard says, sharpen some old hack saw blades to get your rhythm and technique down. Good luck!
Blessings,
Omar