A few clarifications, and then the reply I received from Vance & Hines. And thanks again for the replies here - they were very helpful - I've been out for a few rides with Autotune and its a nice feature.
The Stage III kit for the '17 Dyna Low Rider was difficult to find, and it is part number 92500028. It was a 103 to 103 upgrade with more compression and and a 585 cam. At the time there was no upgrade kit with more displacement, but HD does now show a upgrade kit, not yet released, 92500039, that is a 103 to 110 conversion.
I had my dealer perform the 9200028 upgrade, and they installed the FP3 and applied a V&H map.
Here is the replay from V&H:
If you change the air intake, all you would need to do is re-flash your base map. This will clear the ECU's adaptive fuel values, forcing it to re-learn for the new intake. To do this, go to 'view/edit maps' and press the map in blue. Then, press the lightening bolt in the upper right corner.
FWIW the only Dyna model 92500035 is valid for is the Breakout. There are so many Stage III kits, I spent a lot of time looking at each one only to find it would not work with the Low Rider, and at the time the only kit that fits the Dyna Low Rider was the 92500028.