That is a lot of work to do to install a transmission that is pretty old.
Sometimes we have to do thing forced by economics that we would not prefer
to do otherwise.  If that is your situation, then you have few alternatives.

Have you looked into having a local shop (not a freaking dealership nor
worse
still a franchise operation) freshen up the used tranny?

I would prefer used to rebuilt - ie., untouched since it left the
factory.
Typically 6 cyl. transaxles don't last as long as the 4 cyl. (more
torque), but depending upon how often the fluid was changed and how it
was driven, they can last a long time.
If I had to guess a typicall average with no special care - 150K, with
regular fluid changes and sensible driving you might double that.

80k-100k is fairly old. It may be on its way out. With regularly
scheduled  maintenance, these typically last about 120k. Gentle driving
and better care will give you longer service (typically 2x), but these
are inexpensive transmissions and should be treated accordingly before
you spend big dollars.

The V6 transmission has problems with sluggish line pressure resulting
in a lot of wear and tear on the internal friction material. Around
1997 or so they added a booster pump. But the A540 series is never that
great of a transmission.

Consider pulling a low-mileage one without front end damage from the
junk yard for $300 if you are installing it yourself (check model
compatibility first). I heard some chain stores do this to their
customers without telling, with junk yard ID marks still on there.