My allison transmision is making a grinding noise when in gear from the back end of the transmision

Sounds like a bearing problem. The gears are held in place by roller bearings, and they sometimes pack up. Working the machine with a bad bearing eventually grinds up the steel balls or rollers that the flanges roll on, and the bearing collapses completely. The bearing itself will announce its demise with a grinding sound, and worst case scenario the bearing is so far gone that the gears are running out of true with respect to one another, and this could be the grinding you are hearing.