First, when you upload the tune out of your ECU, what is it? How does the fuel compare with the stock TOR R3T tune? What is in the PCIII? It may have already been dyno tuned.
What custom tuneecu tune do you have for R3T with your setup? You don't need to revert to stock to tune the pciii. You just need to make sure the values in the secondaries table in the tune you have loaded are all set to 100% and that the O2 sensor is disabled (check box). If you load a different Tuneecu tune, make sure you have a zero map in the pciii. That means zero trims. Leave the pciii in. After you load the best tuneecu tune you can find, have it dyno tested. If it looks good, leave it. If not, get the pciii dyno tuned. I know a guy with the same setup who got 157 hp with a good pciii dyno tune.