First, I appreciate the discussion on this as I don't want to be posting bogus information. I see what you mean by the location of the clips. And please don't misunderstand me, I'm not trying to say you are wrong in any way. I spent way more time than I probably should have trying to figure this stuff out. But this is a rather peculiar situation.
I went back and looked at some of my notes on this and just double-checked a few things online. In the diagram below, parts 9 and 10 are the same on every Alpha One Gen 1 and Gen 2's from 1983 to 1997.
However Part 12, the coupler end yoke, had 2 O-rings up through Gen 2 S/N 0D869999. Those used u-joint 75832T1. From Gen 2 S/N 0D870000 through 0M400411 the coupler end yoke had 3 O-rings and used u-joint 805536A2. However if since parts 9 and 10 didn't change, it would seem that either of those u-joints should fit with either coupler end yoke, since they both also fit the gear end yoke and center socket. By the way, part 75832T1 runs about $20 cheaper. lol.
I did notice a thread from years ago where someone had posed the question about automotive u-joint parts, the standard response of the Moog 315G etc. was given by Don S. The original poster then asked about the caps sticking out 1/8" to 1/4", to which Don S. said that not uncommon.
Therefore it would seem that the list I showed earlier could possibly still be relevant.
I can't say what the situation was with you not being able to get the clips in. Could the yokes and/or center socket have been aftermarket parts and possibly not identical to the OEM version? I'm just hypothesizing, because it seems that other people got those to work with the same coupler end yoke as you should have but....I don't really know.