Live-data can save a lot of guessing. Look at "turbine speed" to see if the TC is passing torque through to the trans, look at "gear-selected" to see if the shift lever is moving the shift arm on the trans properly, look at "gear commanded" to see if the PCM has (for some odd reason) inhibited trans operation.
If in doubt about the shift linkage, simply disconnect it and manually put the trans shift arm in its detented position for the gear desired; see if you can get it the beast to move like that.
This is a rebuilt... did it ever work after first being installed? Have you contacted the rebuild/install shop?