To set the level I first run the car on the road for a couple of minutes. I shift it through all the gears. Unless it is a very hot or cold day that seems to put the fluid right in the proper temperature range. Then again I am only going by feel but the 90-130 degrees range seems easily "feelable".

To answer you question, NO I would not have someone sit in the car and put it through the gears while I am under there adding fluid. This is not safe and there is no reason to go through the gears again. To repeat the engine has to be running when doing the check (i.e. the car in park, the brake on, in a well ventilated area, etc.).

Given that your fluid looked "bad" you fit the classic problematic situation of changing fluid in a high mileage tranny. Do yourself a favor and read up here, or do a Google search, as this is a common problem on any vehicle. Not saying you have these issues but your sure may have and this can ruin a tranny.

I still think you need to triple check your level first. If that checks ok and the problem is still there you may need to do something like flush the tranny and do another filter change. That could help to fully dislodge/remove the junk recently loosened, and now lodged heaven only knows where, by the new fluid you just added.

Just my hopefully helpful $.02.