Forget about using the factory tool.  When installing the axle through
the seal, be sure to guide it in carefully and avoid any contact with
the seal if possible.  Support the inner joint with one hand to
accomplish this, while feeding the shaft towards the transaxle with
your other hand.

Once the joint is as far as it will go into the trans without force,
spin it back and forth while applying light pressure until you feel the
axle splines catch on the matching internal splines of the side gear.
To verify that you are partway in the splines, you can attempt to
rotate the shaft -- if the opposite side axle turns, you are there. (Of
course the other side wheel needs to be off of the ground for it to
turn)

Now keep pressure on the inner joint and try to keep it as centered as
possible with one hand, and push the axle towards the trans with the
other hand with sharp blows until the inner joint goes all the way in
and seats it's C-clip.  This step uses the inner joint's plunge action
as a kind of slide hammer to facilitate compressing the C-clip.  The
steadying hand must do it's job well, or you may damage the seal if the
joint were to pop out partially during this operation.

Make sure the differential resevoir (if separate) or trans is full of
oil when you are done.

Toyota MDT in MO