Not too sure on the 1st gen but I suspect a tranny cooler for the auto, larger battery, higher amp alternator, hitch, 7 pin wiring and a different fan clutch.
I had a factory towing package on my PreRunner 1st gen. I got none of that stuff. I also only got a 4 pin trailer harness which was recalled due to it catching on fire. Had it replaced in '06. It did get the hitch and when they replaced the trailer harness they forgot to hook it up to the truck which cost me at U-haul when I was out of state to trailer a move.
I took it to a Toyota dealer where I was at and they refused to work on it, when I got back home I went to the dealer that installed it and they had went out of business. Go Figure!
I got the last laugh as I made a ton of money when the frame failed and another Toyota dealer bought her back at bluebook + 1/2. Huge profit!