The d20 shown in my pic is a "side-fill" unit. I have a freshly-built d20 on the shelf now for a tf 727 application (proper intermediate gear) that is a rear fill and came from what I believe is a '75 sii.
The 727 was not available in a Scout II until sometime in mid-1972 calendar year.
All the d20 units use a 1-1/4" idler shaft for the intermediate gear support.
So it's entirely possible that either an "early" case was partially converted to proper Scout II/727 innards (and would be correct if the part numbers match),...or an "early" case was swapped in but contains the wrong intermediate gear for use with a 727 bull gear.
I have no direct experience with the scenario trever describes (I.e., I've never "fixed" one!), but I do know of these units being mis-matched by others, and while initially the package worked ok, the noise/vibration issue developed over a couplea thousand miles and progressively became unbearable.
While the helix angle mis-match is only 2.5*, in precision gearspeak that is a huge difference!!! The "point load" of the gears is enormous!
In case you haven't already found this resource, I think it's currently the best "how-to" regarding the d18/20 case builds:
rebuilding the Jeep / IH Dana spicer 20 transfer case
Print it for reference, it has an extensive explanation of how to remove the rear output shaft/bearing assembly and how to re-install and determine the shim pack. The first time I did a d20 build it kicked my ass too until a pro showed me how not to be shy with a big hammer and a "soft" drift!
Don't despair, even if a gear mis-match is not your issue, you would never have discovered the bogus driveshaft issue until it failed...possibly at 70mph on the highway and could have resulted in major disaster if the shaft left the scene!
I'm leaving here soon to go pick up the fresh-fabbed rear driveshaft for my truck (24 hour service for a fresh build!!!), inna long visit with the driveshaftdude Monday, I learned stuff from him regarding "drivelines" that I'd never been taught over the last 40 years! More to come about that in this thread:
http://www.forums.IHPartsAmerica.com/readers-rides/2945-beaters-third-life.html