When you get the top new it comes with stainless fasteners. The good thing is that most of it not is custom. You can order everything you need from McMaster.com.
The instructions below have the correct inventory of fasteners, you'll have to order in bulk packages of 25 or so, so you'll have extras. The only thing that you might have to make is the "washer plates" but those you can cut out of sheet metal with snips or a metal brake. They are also stainless.
As far as the "special tool" is concerned - its just a screwdriver handle with a flexi shaft and a 10mm socket on the end that prevents you from over torquing the nuts. You can actually get one at Sears.