The Race Tuner (SERT) re-programs the ECM that is already on your bike. The PC-III is an additional box that modifies the signal coming from your bike's ECM. The problem you would have is this: the SERT has altered your stock program, so the PC-III would be altering an already altered signal. The PC-III programs work with specific stock ECM programs - stock, Stage 1, Stage 2, etc.
To use the Power Commander, you'll have to undo the custom SERT program from your dyno run. Next, get the the ECM flashed back to a stock set-up (or Stage 1 if they did that when you got the 95" installed), just as if the SERT was never installed. Now you can install the PC-III and try an existing PC-III program that closely matches your combination of parts.
A competent dyno tuner (SERT or PC-III) may still your best bet since your combination of components may not exactly match any of the Power Commander maps.