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:
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.
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.