Okay so after a long a grueling process of assembling the driver side axle assembly and then attempting to install (learned the hard way not to hit the CV axle with a metal hammer, thank you RockAuto), I keep running into the same issue with the intermediate shaft.

I will insert it into the transmission, and then twist it and push until I feel it slide in even further. I then check to see if the bolt holes line up, and they don't. I have a 6 bolt swapped 2G with the correct bracket around the intermediate axle, but every time its about a half an inch off. I am completely out of ideas, except for one. The intermediate shaft is made of steel, and while steel doesn't rust, you can clearly see which area has been exposed to the elements. Whenever I push the axle in I can still see a bit of the shiny, unexposed area that I would think would be inside of the transmission, but time after time it's still there.

If you have any ideas please comment, and pictures would be 10x as helpful. Thanks so much!