Swapped 8 3/4" pigs, now axles won't seat fully?

I have stock timken tapered rollers, I understand about the whole axle shaft endplay business... why?

Why what?

If the bearings aren't seating, it is very possible as mentioned that the axles aren't engaging the second set of splines in the suregrip.

There are two sets of splines on each side of the suregrip and sometimes they become un-aligned and can cause issues like what you are experiencing. I usually line them up before installing the center section.