Look in the TCC section and there will be a setting like always unlock TCC under this temp and always lock TCC over this temp. Most Peoples Data Logs show NO TACH RPM , this is an input I need to see where your engines are running in which gears, I can not see or hear your trucks running from here...
Connecting to the VSS wire could be your problem- the vss signal is a different type of signal - the PCS just needs a raw speed sensor signal, so use the rear diff sensor and see how that does. Connect (just "y" onto it) the pink/red Ford wire (I think that's the color, but could be wrong) to the orange/red PCS wire. The other Ford wire to the black/white PCS wire. There are a lot of ways you can configure the speed inputs as well. I typically use the non-calculated, raw signal with differential speed inputs- but it can be done with the calculated input as well. Your MLPS shouldn't be an issue as long as it matches your harness, as it must if it plugs in.
The speed signal settings are in the "transmission setup" folder- "speed inputs/gearing chart". I'm guessing that your speed input is configured as a non-calculated signal since when you changed the gear ratio and tire size it didn't help. If that is the case, next to your "driven wheels speed" you will see "speed 2" or "speed 3". With this config, you can lower the pulses per rev number for your "driven wheels speed" and that should increase your speed value.
If the "driven wheels speed" is set to "calculated" then it is all in the gear ratio and tire size and perhaps the change you made before just didn't stick for some reason.
That's about as much detail as I can give you for free on that- hope that helps!