Well everyone, it seems I have hit a nerve with my original inquiry and
thank you all for your responses. After reading over the responses I
think I am going to run both the baseline and proposed fans continuously
(it seems the most conservative case) and use 0.0003 kw/cfm for the
baseline fan energy but add an A value equal to 1.4 to cover the
proposed system Merv 13 filters and return ductwork.

I think I will also modify the EIR cooling equation to use 300 w/cfm fan
power instead of 365 w/cfm power.

So baseline PTAC fan power = CFMs *0.0003 + (1.4* CFMs/4131) which works
out to be 0.00057 kw /cfm for a small 0.83 efficient motor

and baseline PTAC Cooling EIR will have a 0.10 constant instead of a
0.012167

If I ever have to submit this to LEED I will probably regret it, but it
seems to be the most logical approach. Of course logic and LEED don't
necessarily go together.

Oh well, thanks again for the feedback.