Lem....not sure what to tell you.
When you rechecked the level of the ATF, are you SURE that the transmission wasn't already too warm??
You can't allow them to idle but maybe a minute or two, from a COLD start this time of year before cycling through the gears and double checking the level.
If you checked the final level after the transmission warmed up, the fluid expands and it will dump out on you. Leaving it under-filled.
I also have never had a transmission go out on me either, I'm not sure what it would feel like.
I DO know that allowing this transmission to go 180k on it's ORIGINAL ATF is almost always a death sentence; that fluid was long worn out and you may have toasted the transmission as a result of it.
What did the pan look like when you dropped it?
Also, have you tried lubricating your driveshaft...there is a zerk fitting under there somewhere....this could result in clunking.
And how old is your rear differential fluid? If that's original, that could be the problem too.