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Welcome, I'm Chris (aka Moose) I prefer to work when others don't, I am here around lunch and after dinner till after midnight.
Get the shaft splined together. Then give the shaft a swift hard push towards the transaxle to collapse the cir clip and get it then to expand once locked into the differential. Sometimes it takes a few tries. You should be able to tell when it is seated because the seal will be covering the shiny surface on the shaft so it can not leak. If needed hitting the end of the shaft using a wood block and mallet will work as well.
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That pin is supposed to be there. It is called the pinion shaft. It is like the pin through the center of a rear axle differential holding the spider gears in place. You can pop off the clip then insert the axle shaft to see how far it should go in. Then you will know when you have pushed it in far enough with the clip installed. There is also the possibility the prior failures wobbled the shaft like cray and that has worn out the clips ability to spread enough and lock in place.
You need to compare your 2 shafts, they may be different.
The only things to blame for a axle shaft not locking in
I doubt the parts store has those clips in stock, they would probably have to order it.
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Hello again Chris here,