I suppose you can shorten your yoke. It's worth a try. Be sure to chamfer the edge again, like in your second photo, to keep from tearing up the seal.
Also, you can see in your first photo where the yoke was riding in the tailshaft. It looks to me that the seal was riding at the 3/4" mark on your ruler and from the 1" to 2-1/8" marks is where the yoke was riding in the bushing.
http://www.summitracing.com/compare
Here are two yokes from Ford Racing, listed at Summit. The measurements for the total length of the yokes are included. I still think, for the money, it would be best to get a new yoke.