Assuming the trans really does NOTHING at all, no a single movement, not a change in engine idle, not a single strange noise (like a converter not bolted to the flywheel!), then I can think of 2 things:
is the transmission linkage connected? Even an electronic trans can use and need a shifter linkage (4L80E, for instance);
otherwise, I would look into the elctronics: is the computer programmed for a 4L60E? Is everything connected properly? Any wire hanging somewhere? Did you use all the engine/trans grounds?
Electronics/electricity can be annoying, I have 2 old cars with EFI: on one of them, I had forgotten to connect the trigger wire to the starter motor, on the other one, I had forgotten the fuel pump fuse... Each time, it took me some time and some swearing...
