Yeah,
@JohnGalt helped me out there. We adjusted the ride height sensors and all is well. Noticeably better ride/stock like on pavement. Another key note from my experience.... After the work was done none of my drive modes were available. I could manually use 4x4, lockers, front sta bar disconnect and could manually adjust the exhaust, however, I could not adjust steering feel, shocks or transmission/no sport mode/raptor mode, etc...
Forescan was showing an issue with my rear right shock. Upon further inspection it wasn't plugged back in. So I put some dielectric grease on the connector and got it to re-seat properly. It ended up that three of the four weren't fully plugged in. After greasing all four connectors and getting them properly seated, we were able to recalibrate with forescan and all the modes came back and height was adjusted with improved ride.
I don't think it was the shops fault, I think they thought the connectors were in place. I've had this issue on my own with wheel speed sensors, rear bumper parking sensors, etc... In all the cases dielectric grease was the fix. It's now part of my off road kit!

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As a review: My overall experience thus far has been very positive with the 2" Hyperco shocks, FMI no lift top hats and 39" KO3 tires with D sidewalls. The on road manners are essentially stock, which I value quite a bit. Off road there is more stability and functionality. I haven't noticed a drawback to date.