I wonder what pin you removed !? Yikes! When all this is over you probably need to go back and see where that pin belongs. At least on the BX series Kubotas and B2150s (I've worked on half a dozen of them) there is a spring loaded collar around the end of the driveshaft that mates to the mid-PTO under the belly of the tractor. Usually that collar slides along the axis of the shaft outward away from the PTO maybe 1/2" and frees the shaft from the PTO. I don't have a picture handy, but essentially all PTO shafts have a machined "ditch" around the circumference of the shaft which interrupts the splines and provides a place for the locking collars to seat and hold the shaft female splines onto the PTO.
In your rightmost photo (blown up, not in just the small version) you can see that collar (?) in the far right of the image just beyond the rear U-joint. That is your release collar. Some variations
turn to release and some
pull. I can't tell which your's is. HOWEVER...
There is a POSSIBILITY that your older machine does not have a release collar and maybe I am looking at the housing around the PTO rather than a release collar ?? Can't tell. That would be consistent with your and BG's discussion. If that is the case, then maybe you really did need to remove the pin as you did. IF THAT IS THE CASE use penetrating oil and soak the splines, let it sit over night, and try again to remove it. The splines may well be rusted and you might have to tap the U-joint yoke with a heavy punch to get the u-joint female part to move on the PTO shaft. Just enough to break the rust.
For sure as BG said the entire drive shaft and U-joints stay with the mower deck NOT the tractor.
My
B2150's were made in about the same years as your
B6200 so it would seem strange if the belly mower connections were different -- but of course they could be. Let us know of your progress & good luck on it.
I see you mention that the deck is a RC4862F . Tractor Data website shows the 48" belly mower for the 6200 being a RC4862
H rather than
F. I wonder if that indicates some drive shaft difference?