...Gotta school me up on not trying to align the motor with the rear axle; I thought this was optimal.
Nope. Not necessary. Broncos didn't come that way from the factory, so it's not necessary after your change.
As Steve's descriptions are showing I assume (although I admit to not understanding, or read all of it myself%)) there is even a minimal angle required. And it's not zero.
So there is always supposed to be at least some (1/2° I believe?) angle to let the joints move and keep the grease and needle bearings happy.
Not many vehicles have a really straight shot between the crankshaft and the rear pinion. Low slung cars will be close, but still have that offset to keep the u-joints working over the long term.
And your rear pinion is in constant motion anyway, not including suspension movement. It rises under load and falls under coasting situations. By a large amount sometimes.
On a single-cardan style shaft (one single u-joint at each end) you "could" try to get it close, but it's not needed as there is quite a bit of leeway. Look under any truck, old or new and you'll see the angles that different manufacturers are choosing to use.
While you can have a bit of angle to the shaft, both joints should be at the same relative angle to the shaft (within a couple of degrees of each other I think?) under at least it's neutral condition.
By that I mean that the rear output shaft of the trans, and the rear input (pinion) shaft of the diff need to be very close to parallel to each other, but their height can be offset, which puts the driveshaft at an angle between the two.
A double-cardan shaft (where the front/upper joint is a double-joint assembly and the rear is still a single joint) can have the shaft at an even steeper angle in regard to the upper joints and the trans and diff angled no longer have to be parallel. In cases like that (such as with the stock Bronco shaft) your output shaft can be many degrees off of the centerline of the driveshaft, but the rear pinion angle should be 1 to 2 degrees down-angle from the centerline of the driveshaft. This allows for the up and down motion of the pinion ("axle wrap" or "pinion climb")
This is the earliest known version of a Constant Velocity joint.
Basically, no Bronco came from the factory with a straight shot from the transfer case to the rear axle, so even after changing to 2wd, yours doesn't need to either.
And all that is not to take away from reading Steve's/Ford's technical diagrams and descriptions. Still good to know the low down and dirty technical details.
Paul