I'm currently building a minimax 1030f. I have been plugging away so far for a total of 10.5 hours and have both sides of my fuselage built and ready for epoxy. I was very careful in using a belt sander to get my final dimensions without burning the wood and getting it brown but it's almost so smooth that it looks polished. What is the recommended way to prep the surfaces before applying epoxy and clamping?

Back in the bad old days before epoxy; it was recommended that the surfaces of the joint be scored with sharp chisel corner in a cross hatch pattern. I think that it was suggested when the glue of the day used lots of clamping pressure. Today's epoxy does NOT require high pressure. Perhaps you could try the scoring method on some very smooth scraps and then break the joint to see how it worked.  

I wiped all my joints with a cloth dampened in acetone to remove the sanding dust.

If you are using WEST, you should ideally pre-coat areas to be joined with unthickened epoxy, then use slightly thickened epoxy to join. This is particularly important for end grain joints.

I have the recommended T-88 epoxy.

Agree with ace...just wipe the dust out.  T88 recommends sanding Doug fir due to opening up the resinous nature of the wood and wiping with lacquer thinner.  They recommend a freshly planed surface for sitka spruce or pine.  But if you can sand fir, you can sand spruce or pine as long as you remove the dust.