I had to replace my stock steel driveshaft.
The replacement shaft had rust scale inside the female splined trans yoke on the shaft, but I have since gotten most of it out naval jelly/wd40 and sanding & small thin files. I am stumped as to why it will not go in all the way or at least another 1.5 inches so I can bolt it the rear end. The old yoke from the first shaft slips all the way in without any real force. My shaft has an area of splines that looks like it should have a keyway on the shaft but everyone here says orientation dont matter, but when I rebuild the trans I didn't notice anything on the output that was out of the norm, or at least I don't remember it.

 

I had the same problem but it sounds a though you've done what's needed to solve it. I soaked my yoke trans fluid, cleaned, lightly filed, cleaned again with trans fluid and in it went. I guess this doesn't really help you any. Any chance that it is the wrong yoke?
Jon

 

find a friend with a bead blaster and clean out the inside of the yoke properly.
or just put your old yoke back on with a new joint.