VERY LONG UPDATE:
An update for anyone else thinking of doing the complete fluid flush on the 5-speed auto.
First, a big thanks to Gimp for suggesting removing the front driveshaft. I remember thinking the last time I changed the tranny filter that if I removed my front differential, I would loose all of my fluid from the transfercase. Nope, the CV joint between them keeps the fluid in the case. I did try again to remove the catalytic converter under the tranny, and once again, I couldn't get it off. I ended up rounding one of the bolts between the cat. and muffler so I gave up on that idea. I removed the front driveshaft (very easy!) and then started loosening up the bolts on the pan, removing the rear bolts completely. When the fluid started draining, it reminded me why I removed the tranny cross-member the last time I replaced the filter. The fluid runs all over the cross-member and spreads the dripping out over a 2 foot section (much bigger than my drip pan

). So I put some bolts back in, tightened them up enough to stop the flow and removed the cross-member. I did think to cover my catalytic converters and exhaust pipes this time with aluminum foil so that I didn't smell burning tranny fluid for the next two weeks.
Anyway, with the cross-member removed and the transfer case skid plate, I removed the bolts again. I supported the tranny by my floor jack this time since the last time when I let it drop down I had to put the jack under it anyway to get the bolts back in. The 5-speed auto only holds 4 quarts in the pan and that is about what I got out. I put in the new filter and tried torquing the bolts to the 30-41 ft/lbs that my older edition ('94-'98) Haynes manual recommended. At about 25 ft/lbs it felt like the bolts were stripping. I decided to stop at 25. (Jumping ahead here: I remember reading a post from someone else recommending the newere edition of the Haynes manual so I went and bought it to confirm the torque settings. It listed the torque settings at 108-140 inch/lbs. That works out to about 10 ft/lbs. No wonder the bolts felt like they were stripping. I backed off all of the bolts to the correct torque and made sure there weren't any leaks).
Back from the future now: With the pan correctly torqued, I moved to the front. I bought 6' of 3/8" hose (only needed 2' though) and 10 additional quarts of Quakerstate 4x4 Mercon V (cleaned out Walmart). I disconnected the outside hose from the tranny cooler to the tranny and let it drain into a 1 gallon milk jug that I marked 1 qt, 2 qt, 3 qt and 4 qt on it. The metal line from the tranny drained a bit also. Next, I took the original hose off of the tranny since it wasn't long enough to drain into my milk jug while it was on the ground and moved it back to the metal line going to the transmission. I put the new 2' section of hose on the tranny cooler. I stuck the end of it into the empty milk jug. The other line I stuck into a new bottle of Mercon V, hoping that the tranny would suck it in while it spit the old fluid out. I figured that if it worked, I would fill my 5-gallon bucket up with new fluid and go from there.
I had my Wife come out to start it for me, waiting for me to yell to shut it off is something went wrong. My yell came a little sooner than I expected. The fluid was draining into the empty milk jug like I expected at the rate of about 1 quart/minute. Unfortunately the other line that I hoped would suck up the new fluid, was draining fluid back into the new bottle as well. It didn't take long before the full bottle of tranny fluid was even fuller and soon running down my hands and all over my garage floor (that is when the yell came). Well that didn't work, so I looked for a plug (I used a 3/8 bolt) and used the hose-clamp to close the end of that hose. This time everything worked. I would just have to poor one new quart in through the tranny fill hole after each quart of old fluid came out. I had my Wife shut off my Explorer after each quart, continuing the process until I was out of tranny fluid.
I had hoped that the 15 quarts that I started with would be enough, but even after 15 quarts the fluid was still coming out quite dark. Off to Walmart (different Walmart) to buy 5 more quarts. I repeated the procedure with the last 5 quarts. It still didn't come out as clear as I would have liked, but at least when I shook the bottle around, the residue left on the inside of the bottle was red instead of brown like the first several bottles.
I put the hoses back on and checked everything over again for leaks. No leaks so I went for a test drive. My tranny seems like it might be shifting a bit smoother although it is hard to tell with my Superchip which makes it shift firm to begin with. I do still have a harsher shift when going from 2 to 3 than the rest of the shifts, but that has been there since 25K miles. I am now at 82K miles and first changed just the pan fluid at 50K per my '97's Owner's Guide and Extreme Duty Service Interval. Since all I replaced at 50K was the filter and 4 quarts of fluid, I decided to the the whole thing this time. Considering how dark the fluid was, I think I will stick to 30K intervals from here on out, especially when considering the full fluid change was actually easier and less messy than the filter and 4 quart change.