I drained the fluid from the car after letting it sit all weekend. Got about 3.5 quarts of very brown fluid out. I put back in two quarts and ran the engine for a few minutes, then drained it again. Filled it back up, then pulled the fluid cooler return hose off the transmission and alternated running the engine and filling the transmission back up. After about two total gallons of fluid, it was running pretty red and looking good. I put two quarts in and let it run for a minute or so - the malfunction light went out of it's own accord. I ran it through the gears a few times then shut it down. MIL stayed off, so that's an initial positive. Need some more ATF - it's still a quart or two low, but it's solid progress.