It also seems like Intamin is almost certainly at fault for the currently running 6 of 12 possible trains issue (assuming that is true).
Partially. Most of the reason why limited units are being run is because the ops are still getting used to the ride, as when more units are put on the dispatch interval decreases considerably. The main concern is if there were more units on the ride would cascade like crazy if there was so much as a minor delay in the station.
A cycle is 3.5 minutes, 12 units, that's a 20 second interval between trains.