Alignment tools are not always accurate. The BEST alignment tool, bar none, is an old input shaft, and if possible, one with a collar adapted to it to pilot right in the bell center hole.
Sometimes I used to leave the clutch cover bolts loose, and if I had trouble, I'd pull them out "sloppy and throw some longer bolts in the holes to allow the disc to move. This was pretty extreme, and soon after...............I scored a pilot shaft!!!! LOL
I had the box in/ out of my old 383 RR several times, now THAT is a story...............and it was done every single time with the front end on big blocks, and a floor jack for a trans jack.
The rundown..........
1.....The box ate the main center ball bearing unknown to me......I was inexperienced at the time.
I ran it until it damage the nose of the mainshaft.
San Diego Machine talked me into repairing the mainshaft with a collar. New bearings of course
put it together.
2......The collar failed. A piece ate about 1/10 of a corner of the cluster.
Pulled it apart. New mainshaft. Left old cluster
3....Cluster failed, took out the mainshaft and the cluster.
I lost count. How many times is that?
By comparison, the V code 70 had the box out twice, for new clutches, and replace the bearings in the box. Side cover off once for a broke 3-4 shift fork.