Replacing U-joints

Yes i agree it sounds like the U-joints.I realize you are mostly stock but keep in mind i changed my U-joints 2 time with the heavy duty ones before getting the FRPP aluminum drivesaft.It olnly cost me 179 from summit,the ride quality is nothing short of amazing compared to a stock unit.?????Just my thoughts.....

Shape, it is not too bad a job. your aod probably takes it easier on them than some stick drivers.
ill share what i know, though i know you know what is up and turn a good wrench.

for testing: you know to grab each yolk and twist them against eachother. i have experience (in Seattle) of them testing fine that way, but having corroded from the inside out. i was getting some squeak with the rear joint.

for doing them: i am lazy. to get my shaft out, i have to yank exhaust stuff. i do them with the DS on the car. hit them with some PB Blaster, etc to make the spyders come apart easier.

unbolt the DS from the rear end. mark the DS and pumpkin flange, so you can bolt it back up the same. also i like to mark any two parts that come apart, like the DS on either side of the u joint. so when it goes back together, it is oriented the same. they are dynamically balanced, and i think many people that have vibration problems did not mark each part they took apart. (no offense, as i bet shops dont mark them, and the problem was there before we got the cars. i think the repair manuals omit this step).

anyhow, DS flange bolts: 12mm, 12 point socket is needed (a good one. if you dont happen to have a good one, buy a nice one. if you round the DS to pumpkin bolts, that is a pain). the bolts are tight, factory has loc tite on them. i use an extension and 3/8 ratchet. some folks use their leg on a breaker, etc. i am a big guy, so i dont fit well, but if i can reach, it comes off. LOL. apply e-brake and break two loose. undo brake, and rotate DS. duplicate on last two bolts.

once unbolted, you can either use my favorite (you know, the 4 pound swinging press) and a socket that is just smaller than the caps on the joints. pound one in, take the cap off, then pound another (90* from the first one). remove the cap, and now pound the last two as necessary. there are different ways to do it, it is a logic and look as you go thing.

carefully take a cap off the new joint and slide the joint in. inside the cap are needle bearings, dont mess them up. i actually buy an extra joint so if i mess one up, i can use the extra and put the first one together later when i feel like it. just me.

both front and rear should be the same. the fronts tend to go out half as often as the back joints.
im sure you have researched the aod's, but i will share this. My g/f's 94 camaro (aode) clunks when coming to a stop. i eventually read that it is normal. nothing that can reasonably be done- it is intrinsic to the design. i dont know if the stang aod's have any similar ideosynchracies. sounds like these are new symptoms, anyhow.

also, if you need two joints, and have any vibs, i would get an aluminum DS. they can be had for 140 bucks. real nice piece. some aerostars had them too, as i recall. i dont know if they bolt right in.
if you yank the DS out and do it on a bench (most manuals recommend this), you may lose some atf (manuals lose gear oil). if so, remember to top up.
loc tite the DS to pumpkin bolts (the 12 mm, 12 pointers). they like to back out.

on pushing the old joints out, in addition to the hammering method, i have used a 6.5" C-clamp with a socket on the cap, also (substitute clamp for hammering). next time, if it fits, i will use a ball joint press. they have one that is a big C clamp. you can get this tool loaned from autozone, etc. i used it on ball joints and it worked great. i bought one since i liked it so much.
i say this, since once you start, you dont want to bend your only clamp and be SOL. nice to have more than enough stuff to do it. you know.
that is all i can think of. easier than what i made it sound like. good luck, Shape.

while you are under there this weekend, might double check rear end fluid level (and trans). whining is weird.
also worth checking the trans mount. since you have had front wheel drives before, you know how important the mounts are in maintaining proper driveline geometry. you also get some clicking and movement in the mounts if one of them breaks (esp the trans mount). our set ups are a little more favorable in that regard, but i think a broken trans mount could allow the clicking you hear. may contribute a whine since things are not quite as lined up as they should be.

sorry if i was ambiguous on the G/F's camaro. i cannot remember what the actual cause is on that one, but i remember reading that it was normal and deciding not to worry about the clunk.

sometimes cars clunk when the TV cable is out of adjustment. i dont even know if you have a TV cable, but as i recall from some of the AOD threads, you are all over the adjustments and stuff like that to check.

i was just trying to toss out some other ideas of things to check while under the car in case the U joints look great.

trans fluid loss. i had my car's rear as high as i could get it and the static fluid level of the trans is slightly higher than the slip yolk hole, so i still lost some. i would have the get the car up much higher than i can to avoid that. no biggie, just wanted to toss it out. sometimes i get scatterbrained and forget to top off a fluid i lost some of. you are right, jacking should minimize the loss (if any on your AOD).

i have had a hard time with rear end clunk diagnostics in the past. hard to pin point the source sometimes. i do what you do: get under and play with stuff. it could be shocks, i have no idea. i have never owned an automatic. sounds like a good idea and something to check. good luck, Shape.