Just a quick comment...I had a similar issue on a rebuild....turned out to be that hooking up the driveshaft put just enough drag on the transmission gear train to stop the gears from freewheeling, even when the box was in neutral. Figured there must have been some drag from the pilot bushing that fed back and kept things inside the box moving just enough to make her "talk." Had no more noise once we bolted on the driveshaft. Whodathunk!!
Dave