I am using Raka slow setting
: epoxy and wont be able to get back to it until hour 36 or 40
: after the last coat of epoxy. I have been doing a coat every 8
: to 12 hours to get chemical bond.

: How many fill coats of epoxy do you use and much do you rely on the
: varnish to level things out?

Jason-
I don't have anything much to add to the excellent advice you already gotten.
Many of the 'standard' descriptions of kayak/canoe glassing (stating 2-3 fill coats) assume you are using one of the more 'syrupy' epoxies like WEST, which build quickly.
I haven't used MAS or Raka epoxy, but I did do one project using lower-viscosity ColdCure years ago, and found that viscosity makes a big difference.
You will probably need more coats of epoxy than you planned- you don't want to be sanding through the glass.
Some good info can be found here:
http://www.oneoceankayaks.com/Epoxresl.htm#thickorthin

For sanding, use a fairly hard, long-ish sanding block for most of the work. Lately I've been using scrap insulation foam- cheap and light. Don't be afraid to use a fairly coarse (80-100) grit paper in the early stages if you are taking down ridges,then move to finer grits in later stages.

As has been stated already, you want a smooth, matte, sanded surface with no shiny spots or dips before you think about varnish. Varnish will only accentuate flaws in the prep, not hide them. (Don't ask how I learned this!).