Todd, good luck with your repairs. I know what you mean about doing things your own way. I think the set screw idea will work to retain the yoke but I would make sure that you get full depth on the drive shaft into the bearings on the adaptors on the engine and rear end. I just cannot see how that shaft could have came out of there if both ends of the shaft are piloted in the bearings and the coupler on the rear end was on the input shaft all of the way. You should have to move the engine or rear at least 1 inch to get the shaft out. Is it possible that the shaft is too short? I am sure you will work it out.
Tom