The power steering fluid gets black from the aluminum in the power steering rack. It seems more common on the early ones (95 and 96). It doesn't mean that there is excessive wear, only that the aluminum alloy used tends to shed just enough to discolor the fluid. Once the fluid is black, it will take several flushes to get the black residue out of the steering rack. Also, it will discolor again no matter what you do. The balck color doesn't really seem to hurt anything but I would rather not have it there in my car, so if I were you, I would flush the power steering fluid about every 15,000 miles to keep the residue to a minimum.
The transmission problem could be from the MLPS (Manual Lever Position Sensor, also know as the Transmission Range Sensor, in days of old, known as the Neutral Safety Switch). When the MLPS gets old it may be telling the PCM that you have selected a different gear than you really have so that this message can come up. If replacing the MLPS does not solve the problem, then it is probably an indication that the trans is starting to fail.