This is not really going to answer your question and is really sharing my experience with the Power Commander on my FLHTCUSE3 yesterday. The bottom end range is really lean and pulling out is always a challenge with lots of clutch feathering and simultaneous rpm revs. Not what I have had with my FLRHSE2 and the SERT which has been flawless for 5 years. Dealership spent about 4 hours on the dyno for the bottom end and then came and told me the PCIII is incompatible with my bike-this from Power Comander-their position is the failure is vehicle specific. HUH???
Bottom line the dealer is installing a SERT at no charge and will dyno the setup at 1K miles. Does this sound at all right to anyone with more knowledge than I??
Ended up back on the stock ECM for now and the bottom end is better with the mileage still under 25 MPG.
Mods are simpley Stage 1 and Rhinehart Tru Duals
Sound off before I install a 1/4 stick necxt to the ECM 
My thoughts on piggie backs or addons such as the PCIII, which they are good, is that when you add something like this it sends a false signal to the ECM with time 2 or more years later they can give you trouble

I have seen them lock the ECM down and it will have to be replaced a few times. I like to program the ECM so that it is in full charge of the settings you want to see, a good tuner can set up the SERT to give you top performance. The only thing is you need to know what changes he makes to you canned map, have him print it out any changes he makes to your base map, the AFR, timing curve front and rear, and VE front and rear etc. I have not found a way to read the changes made on a map after its installed, it would be nice to be able to pull it out, change a cell or two and reprogram. When I set one up I normaly use the same AFR in most of my cells, changing the VE for performance, and the accel and decel enrichment, I set the the AFR lean and the timing down in the 750rpm and 20, 30 MAP cells for a better starting warm engine it lets the engine crank up quick and gets it off the starter. Like I was saying a good tuner can give you top performance and 95% of the time that is what they are looking at on the dyno, not thinking of the other things that come into play with a good starting and running bike.
With your mileage under 25 on a stock ECM, I would be in question of it in its self. Did they do a total reburn of the ECM after your PCIII was taken off or did they set you up rich until your SERT is dyno tuned? Hope this helps