No issues that I am aware of and I was on the 2,000 mile (4,200 km) trip, driving it to Arizona. Matt did look at several options for rotating the pinion up and we discussed using shims if the need arose. All good for now and the truck will be back in his shop in a few weeks, so we will check over everything at that time.
EDIT: If I recall correctly, the output yoke and the pinion are supposed to be in the same plane, with the drive shaft (prop shaft) connecting the two. We are running bog standard U-joints, not CVs, hence the flat pinion: