I changed my rear end to a Dana so I need to change my driveshaft length. How far into the trans does the yoke need to be inserted before measuring how much to shorten the shaft?
Dr Diff advised me to bottom it in the transmission and then slide it back out 1 to 1 1/4 inch. Make sure the seal isn't holding it back from bottoming fully.
On a side note, verify your engine/transmission center-line angle is in proper orientation to the pinion shaft center-line. They should be parallel to each other after the nose of the rear-end lifts under power. (pinion should be a degree or two nose down when there is no load is on it).
My local driveshaft shop has me insert the yoke fully, pull it out 3/4" - 1" and measure center to center on the u-joints with the car sitting on the suspension. It's always worked for me.