I do hope that you got your issue taken care of.
I would like to give a few pointers though....
You never stated the vehicle. Hard to give good info with no info to start with.
GM did not have a 4L90e. It would have been a 6L90e.
You said that it was controlled through the BCM? More along the lines of the ECM. BCM is body control function. Cruise would go through BCM to ECM.
GM had the 4L80 and the 4L85. The 85 series being the heavy duty variant with a 5 gear planetary. Usually in the 3/4 ton Suburbans as the Allison was to tall to fit in the tunnel. Side note, the Allison with the straight cut gears were a very noisy setup, good but noisy.
Tow/haul mode. Should not use it unless towing a trailer.
The computers will "learn" how it needs to shift. If you run it empty and then tow a trailer it just does not seem to know what to do. If you have the capability, with a scan tool to do a complete drive cycle relearn when you hook up the trailer. Trust the computers to figure it out.
2006 3/4 Suburban 8.1L. I can pass anything, except the gas station.
I wish I had a Duraburb.