When I did my 4 speed swap on my 71, I just had my original driveshafts retubed at Englewood Driveshaft, so the yokes and flanges stayed the same. Based on what I knew at the time about the different companion flanges and the issues in matching them (see last paragraph), I figured this would be the least brain damage, and indeed this was a very smooth part of the tranny conversion.
4 speed yokes are bigger than 3 speed yokes and the u-joints are different. The 3-speed yokes retain the u-joints with circlips, the 4 speed u-joint races just press in.
To top it all off, there are about 3-4 different companion flanges (and mating yokes) used on our older Land Cruisers (and mini trucks and 4runners, some of which will interchange). There was an excellent article by Rob Mullen in Toyota Trails in the late 1990s which showed all those different companion flanges, with measurements and month/year of production identifying which was used when and on what kind of Toyota.