When you are fitting the engine/gearbox into the chassis, it’s very difficult to see if the 2 shafts are aligned.
A short piece of 3/4″ water pipe slipped onto the propshaft spline with give you an accurate assessment before tightening the 2 self aligning bearing bolts. You may need to elongate the bolt holes in the chassis a little. If they are nipped up sufficient to hold the bearing in aligned position, you can pull the engine forward enough to get in there and tighted the bolts fully. (Click pic to zoom in)