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Looking at the spline misfit, it makes one suspicious that there is a very slight miss alignment through the transmission.
Often splines are used to allow for such unless they have an interference fit.
Use of some material to fill the gap generally does not work as the filler is softer than the parent metal. In your case, the shaft is harder than the damaged spline. Using some loctite product will not last long & then bits will float around & maybe block a control valve.
Probably some thing in the planetary is not perfect & the misalignment has shown on the spline.
You cant make everything rigid as there must be room for expansion & contraction, misalignment and end float movement.
As to what to do, if it was me, I would probably rub the sharp edges off & put it back together. I am a firm believer that unless its broken, dont try & fix it.
We have an old scraper here with a 6 speed Allison trans, some of its splines are much worse than yours & it has done many thousands of hours since it was last in pieces. There are no flex disks in the drive line either & it has a lock up on its torque converter so the splines in the trans get a beating.
Did the car have trans problems before you disassembled it ?
Was there clunking on power off/on ?
It would appear that the trans has probably spent much of its life changing between the intermediate gears & not much time in 4th.
Given the relative low mileage of your car, I wonder what has been going on to cause this & the other issues that you have uncovered.
As to our friend with the trans that has lost its splines, it must have been running bad for many 10's k miles to get like that.
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Grumpy Old Diesel Owners Club group
I no longer question authority, I annoy authority. More effect, less effort....
1967 230-6 auto parts car. rust bucket.
1980 300D now parts car 800k miles
1984 300D 500k miles
1987 250td 160k miles English import 
2001 jeep turbo diesel 130k miles 
1998 jeep tdi ~ followed me home. Needs a turbo.
1968 Ford F750 truck. 6-354 diesel conversion.
Other toys ~J.D.,Cat & GM ~ mainly earth moving
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