I have the countershaft and mainshaft back together, however the countershaft bearing in the case seems to be hitting the final drive gear when I put the diff back in. It's a new mfactory lsd, which shouldn't fit any differently than the stock diff, right? The bearing doesn't seem to be seated as far as the main shaft bearing but it does line up with the castings for the plate that acts as a retainer for the countershaft bearing. I've tried a brass drift punch to lightly tap around the outer edge to ensure it's seated, but no luck. What am I missing? Should the bearing sit flush with the case?

 

It appears that your ring gear is upside down in your pic above. The mounting surface that meets the diff. mounting plate is offset... the long/deep side faces up in the photo above and the shallow/short side faces the diff body and the bolts that affix the ring gear to the differential.

 

Thanks, I could've sworn I took it off and put it back on the exact same way, but took a look and the chamfered side was facing up. From the above I gather that the chamfered side should mate up with the diff?

Edit, I haven't looked very closely yet, but should there be marks that line up on the final drive gear and the diff? I don't see it mentioned in other DIY videos. Just want to make sure I don't miss any other steps.

 

No, the marks on the ring gear do not line up with the teeth on the counter shaft. The mark/s identifies the diff body size and ring ratio. The drawing from the FSM above that you have posted shows the offset tooth length in the small circle on the left showing the orientation that I have described above. As you can see, the deep side of the ring gear faces down toward the bottom bearing and the shallow side faces up toward the speedometer gear ring.