Up through 1995, the transmission was a 47RH. In 1996 (and later) 2nd generation trucks, electronic control changed the designation to 47RE. I had a 1996 V-10/47RE 3500 dually.
Sorry that I can't address specific differences between the 1997 and 1999 versions of the 47RE, but I would think there would be some based on the differing characteristics (RPM range, shift points, etc.) of the 12 versus 24 valve engines.
Rusty