FWIW, the 6L80 is also based on the ZF 6HP design as well though with a few additional changes to put the TCM on the Valve body and using a different style of Pump (Vane vs. Gear).
They do make controllers now that allow a 6L80/6L90 to talk to the aftermarket ECM's as well
http://www.zerogravityperformance.com/product/tcm-2650-mechatronic-transmission-controller-6l80e-6l90e-6l50e/