I have no idea if the yota axles are similar to ours but I did find one thing that caused a similar issue with the VX.

When putting the axles back in, the passenger side wouldn't insert all the way into the housing. It turned out that I had installed the bearing backwards (see page 5 of the attached pdf). The offset of the external C-Clip was just enough to cause the whole thing not to button up correctly.

Hope that helps.