OK, after much stress over "did I just screw up my bike", things have been sorted out. The TuneECU documentation is not the most clear on this subject but the software works great after you figure out what to do with it.
To change the Primary TPS, here are a few clarifications that I hope will help the next Captain.
1. Change out the Primary TPS as described above until you get to the voltage setting part.
2. Hook up your computer with TuneECU running and turn the key on. DO NOT START THE ENGINE. (You may want to prep by removing the 20 amp headlight fuse to save your battery.)
3. After TuneECU has connected to your bike, verify the connection by clicking on the Diagnostics button in the upper right corner. This will open the Diagnostics page and gather some readings from the ECU. You might want to note the value for the Throttle setting, however, DO NOT USE THIS VALUE TO ADJUST THE TPS VOLTAGE. This is where I made my mistake and the Idle Stepper Motor was out of adjustment.
4. Now click on the Tests button in the upper right corner. You will see the Tests & Adjust section on the lower left of the screen.
5. To set the Primary TPS, double-click the "Adjust ISCV" checkbox.
SIDENOTE: this is a weird software interface. A checkbox implies a single-click to "check the box", i.e. turn it on. It was a little aggrevating trying to sort out this interface.
6. The checkbox next to the "Adjust ISCV" text will turn solid and whirring sounds will start coming from your bike in the area of the throttle bodies. You will also notice that the Cyl 3 (bottom) MAP guage has changed to read the TPS Voltage.
7. At the bottom of the window some text will appear instructing you to move the TPS until the value reads .060 in the digital part of the gauge and that the arrow is centered at the top. Make adjustments as necessary.
8. Double-click the "Adjust ISCV" text again to continue with the adjustments. More whirrings will occur and some new text is displayed at the bottom of the window. This time it asks you to adjust the TPS until the value reads .072v. You should not have to move it at all but this is just a verification step apparently.
9. Now you can tighten down the torx screw CAREFULLY.
10. Double-click the "Adjust ISCV" text one more time and it will go through a Reset Adaptives process. The text at the bottom of the window will tell you to wait 15 seconds and tell you when it is complete.
11. Turn your key off and disconnect everything. Plug your headlight/starter fuse back in and start your engine.
12. Pray that you did everything right.