There is no set amount that you take off of a flywheel, you can take off a much as you need to get the surface completely flat. Make sure you clean all the clutch mating surfaces with brake cleaner, IE...clutch disk pads, pressure plate surface, and flywheel. Go to Toyota and order all new snap rings and washers for your throw out bearing assembly, I didnt get new snap rings when i first put my stage 3 in and the throw out bearing assembly fell apart when I was driving.
If your going to use Royal Purple use the heavy stuff, research that though, there a few threads on tranny fluid floating around. I use Redline MT-90