I've been reading up on this, and thought I'd post what I found:

Here are some instructions from two sources. The first source has some
pictures that clearly show exactly where the plugs are. Before:
http://www.binaryweb.com/fordtech/trannyplug/04.jpg

After:
http://www.binaryweb.com/fordtech/trannyplug/05.jpg

He suggests changing the shifter bushings at the same time.  The second
source has some additional details. One detail is missing, how deep to
drive the replacement plugs. I'm planning on measuring the old plugs
and installing the new ones to the same depth.

http://tinyurl.com/94vrf
As you may or may not know, the 91-94 Ford Explorer manual
transmissions have 3 rubber plugs that usually dry up and fall out,
especially at higher mileage. If these plugs fall out, you will end up
having to get your tranny rebuilt. You can replace these plugs without
too much difficulty while the tranny is still in the Explorer.

You will have to remove the front seats, center console, shifter boot
and shifter tower, and all the plastic trim pieces that are around the
edges of the carpet in the front of the vehicle. Once all that is
removed, you will be able to pull the carpet back. Under the carpet,
there is an access panel that you will need to unbolt. Once you remove
this panel, you will be able to see the top of the transmission and the
plugs that are to be replaced.

While I had everything torn apart, I replaced my shifter bushings. The
parts you will need are a washer (E8TZ-7Z120-A), a spacer
(E8TZ-7E018-A), and a bushing (E8TZ-7228-A). Those are the Ford part
numbers, and combined, they should not cost you more than $6 or $7 from
the dealer. Replacing the bushings is not hard, just be careful not to
drop anything in the transmission. It is very important to have the
tranny in neutral before you begin to replace the bushings. (I found
this out the hard way, and the tranny did not have any gears when I got
it back together!) Unscrew the 3 bolts that hold the top plate that
goes around the shifter of the tranny that is sticking out. You will
see the bushing below the plate, this is what you are going to replace.
Carefully remove the bushing, being very careful not to drop any parts
or broken pieces into the tranny. After removing the top bushing and
washer above the stick, pull it out, and there is one more washer that
is in the bottom of the area you are working in. Put everything back
together in the order that you took it apart, but replace the old parts
with the new bushings, etc that you just bought from Ford.

At the time that I replaced the plugs, I also replaced the tranny fluid
with Amsoil Synthetic ATF fluid.

http://tinyurl.com/8p6zt
You will need 3 cup plugs (freeze plugs) Dorman #55-108 or Dana
#219-3052 I got mine at Napa for .29 each and you may as well get the
best synthetic ATF you can buy to change your fluid, because if it is
like mine it won't leak again.  Pull your pass seat, console,and shift
lever.

Peel up the carpet to expose the large floor pan and remove it. Now you
see the top cover held down with 10 bolts. Remove it and pull it
straight up. Now you see the 3 rubber plugs. Cut the ends with a razor
knife and remove them. Replace with cup plugs, drive them in with a
socket that is a loose fit inside the cup.