Hi Dave
I'm with Brain on the bottom seals for the PTO drive to. Don't ask how I learned that when I started messing around with majors many years ago

, as routine if I'm doing them I change both sets of seals, it seems some of them had leather seal material that dissolves rather than rubber compounds like modern seals, by changing them I know 99.9% i'm not going back 3 weeks after somebody uses the tractor and the oil starts mixing. or they don't realize and destroy the top bearings in the gearbox

.
I have seen one super that the collar on the top shaft where the seal rides came loose and it by passed oil between the shaft and the inside of the collar to, leading a guy to think it was the top seal, I found that by filling the gearbox(before I took the pto drive from the bottom) and while it was split from the back end, I changed all the seals to be sure while I was there to.
With that plug in the shaft, im wondering if it was either a fixed part of the end of the welded spline insert from machining. Or a plug that was inserted and used to stop the shaft filling with oil. maybe excessive end float from a snap ring being pushed out the rear pto housing, Or a bad bearing allowing the pto to be pushed back onto the male shaft in the pto drive box by a pto driven implement , with to longer shaft to slide properly forcing it in. Then it's punched that piece out the end

.
I have seen tractor shafts have considerable end float and found the snap ring or the groove busted out before. Maybe somebody repaired it and didn't notice the "plug " or didn't care

.
Regards Robert
A Fordson is for life not just for Christmas !.