If I can get my truck idling well a near stock truck should be a breeze. Here's the process I used.
Unplug the IAC and manually set the idle to get it close to where you want with the truck warmed up
In my case I went right to enabling closed loop idle (using timing as well) control based on the RPM I set previously
Then just set the min rpm for auto tune, you'll also notice you have a new tab to auto tune idle VE
Turn both auto tune for main VE and auto tune for idle as they will swap back and forth once you set the min rpm for the main VE table
Drive around and let it do it's thing, also be sure to swap between drive, park, reverse etc to ensure those transitions are smooth
For me the biggest item I worked on was the transitions from park to reverse or drive and where letting the Megasquirt change the timing helped tremendously. I also fiddled a bit with the Closed Loop idle PID settings, but for you guys with the PiMP I would use the supplied settings to start.
Thanks to both Jamie and Jerry who shared what they had done as it was a huge help.