Following up in case anyone else has a related issue with a 2016 Ford Flex.
It is said in other posts but I will confirm. If you are on Sync 3 v1.0, installing 2.2 first seems to be the solution if you are hitting snags. I was using a 3.0 USB and Ford method. Then a new USB hub fixes CarPlay.
I will probably upgrade to 3.0.20204 ( JR3T-14G381-AX - SYNC 3 APIM Software (IVSU) Database - CyanLabs ) but haven’t yet. Then maybe 3.4 with Syn3. As of now everything functions properly so might just leave it since I don’t use Ford navigation.
Thanks to this site and all the admins and contributors!