Rumble-strip is often used to describe TC lockup shudder that can be caused by old fluid or bad lockup clutch material. Are you sure it is an 3 to 4 shift or is it the TC lockup you are feeling? I suspect, however, management problems. I don?t know what trans was used in ?94. That was within a couple of years of when Ford was shifting from the aod to aode (e=electronic) transmission for some light truck and full-size sedan applications. I don?t know anything about 3-speed. I thought that was over before then. If the shop did not know what it was doing, there could be lots of problems caused by the wrong signals being sent to the transmission.
I suggest you find a Ford truck board if you get no joy here. There are often lots of people that know what transplants are practical and how to do them. Factory-trained techs often don?t have this knowledge because they just don?t try to do this kind of stuff. I would hope that your shop tried something that was in the realm of possible and advisable, but I have fear.