Hi Paul,
It is my understanding that LEED definitely wants you to use the actual fuel (coal) and rate for both the proposed case and the baseline case for the Step 2 model.
I don't know what you should use for efficiency in the baseline case, though. You are right that table 6.8.1 does not have efficiencies listed for coal. Are there any local codes or other mechanical codes that list a minimum efficiency for a coal boiler? Otherwise I would send in a CIR. I searched through the existing ones quickly and did not see any questions on coal fuel. It seems strange though, someone must have modeled a coal fueled building.
Good luck. The district ones are tough. I just finished one and am dreading the LEED review comments!
Allison Gaiko, PE, LEED AP