the bolts they refer to are the engine mount bolts. You will be taking the stock mounting bolts off and replacing them with the bolts supplied by the skyking kit.
I dont own or have personally seen a '95 model but I suspect that every Speed Triple is the same is this respect.
You will need a socket/rachet, socket extender, wrench/pliers (to hold the nut steady while loosening/tightening the bolt), and if the '95's are like the '05's you will need a torx socket, perhaps some others on the board can lend a hand in reminding us what size it is that fits the stock engine mount bolt on the S3.
"Top engine mount bolt" would refer to the mounting bolt at the top/front of the engine closest to the radiator.
Here's a pic of my engine area on the right side after a little accident to illustrate:
