I think I would pull the governor out and check to make sure that it is free as well. Would be on the driver side , a little tophat looking deal with a spring like would be on a master cylinder. Pull the cap off, and slide the governor out and see if the weights move freely. Probably will be okay, but you never know.
As far as flushing the system with the engine running, I suppose you could unhook both lines, have one empty container, and one with fresh fluid and just see if it would draw in the fresh and spit out the old. I guess it would take a bunch of fluid to do it that way.
The TV cable is pulled tight at WOT, right?