OK... I finally took my 4Runner out for a test drive to see if the ATF level adjustment solved any of my complaints about the transmission. Well, everything seems unchanged so far. Putting it into "D" for the first time today, there was a second or two of slipping, then full engagement. It's really strange. During summer I didn't notice any slipping. As temperatures cooled a bit this fall it seemed to start slipping a lot and then fully engage violently at times. Now that temperatures are even colder the slipping is less dramatic and the transition from slip to full engagement is not as bad.
I've got a cold right now so my hearing isn’t too great, but the muffled metallic noise (like keys jingling) I usually hear in 4th gear is still there I think.
The fluid I drained from the pan looked pretty good, only slightly darker than the new ATF. I guess that's probably typical of a vehicle with only 5000 miles on it.