Have you measured the current end play? You need to know that before you start.
If there is presently no end play in the shaft, you need to remove the rear bearing cap, then you need to take the front bearing cap off and tap the shaft so that the rear bearing cup is moved out a bit. then by adding shims and replacing the rear bearing cap/cover, the rear bearing cup is re-seated at the proper depth. .006 end play is just barely perceptible by hand.
If there is currently too much end play, all you need to do is remove a shim from the rear bearing cap..this will re-seat the bearing cup when you replace the rear bearing cap.
End play may not be the issue....
Can you turn the shaft freely without the yoke in place? If you don't have lockout hubs you might have to remove the front drive shaft...and of course insure that the t/c is in neutral.
At which point, when installing the yoke, does the shaft start to bind?
Can you tell if it is the shaft that is binding or is it the yoke?
If it were me, I'd make every effort to straighten the dust cover on the old yoke, and see if I could make it work, as it worked before.
The new yoke might be drilled too deep allowing it to seat too far down on the shaft, allowing the dust cover to bind.
http://www.cj3apage.com/index/Tech_Tips/Model%2018%20Rebuild.htmHere is a quote from that site:
"Since I do not have a run-out gauge I checked it by feel. It should just barley move. If it has no end to end movement at all, it is too tight. The endplay is adjusted by installing and removing shims under the rear-bearing cap. If you are just under the correct measurement it should work out OK when you get to the next step. If you are almost over the correct measurement you may need to remove a shim. I suggest that the measurement before sealing the case should be 0.002" - 0.006" Note: If you have over-tightened the shaft it will be necessary to remove the front bearing cap and tap the output shaft to the rear again until free. CAUTION: Tapping on the front output shaft with the front bearing cap installed can damage the front cap because of the front bearing cap lock-ring."
I really hope you solve this without having to dissassemble the t/c...I just can't imagine how a previously working t/c would need to have the endplay adjusted simply as a result of removing the rear yoke and oil seal....
I just had another idea...could the yoke be binding against the new oil seal?? Could the seal have been distorted when you drove it in, or maybe not be properly seated?