Assuming your rear suspension geometry isn't wacked and only moves the rear axle a minimum amount as it travels,
most set the driveshaft yoke so it's approx. 1" out of the trans when at ride height.
For what it's worth, I just had a driveshaft shortened and balanced by a driveline shop. He had me install the driveshaft yoke all the way into the transmission and measure from center of the bearing cup at the transmission yoke to center of the bearing cup at the differential yoke. That measurement was 19-3/4". He cut the driveline so that the measurement for the finished driveline would be 19" center to center. I've since taken the engine and trans out of the car for rebuild and paint and haven't yet installed the driveline, but figure it will give it enough room to install and not "bottom out" with suspension travel since the transmission and differential are going to be close to the same alignment at ride height.
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