We had the same type of problem with ours, went to the dealership and was told when my wife reconnected the harness some of the prongs weren't connected. Not sure if that's the same solution as yours.
I had a similar problem in my 22 JTR, eventually it started staying on for longer periods of time. Finally took it into dealership and found out there's a handful of sensors that plug into the differentials and could go bad. Had them replace the bad sensor and have not had it happen again.
I purchased and had them installed by a local Katzkin authorized dealer. Between the seats and the Armorlite flooring it has really lightened up the interior.
I've seen a install video of the Kracken set up and it looks very similar with the exception of some of the switch locations. Maybe watch a install video of the Innovative version and look for any differences.
I don't have the Kracken set up but I do have my dual air compressor located under the front passenger seat with no issues. Can't remember which set up off the top of my head. Just looked it up, it is an Innovative AT Products set up