If you need the ports for to do a repair, get 5 inch size. I've made a mistake of putting 4 inch, which are extremely tight if you wand to put your forearm and manipulate inside. Also, do the repair after you cut the hole, but before you install the port. This will gives you extra inch of space, which you will appreciate.
I've got a Hobie port kit a few years back, which came with 2 ports, a tube of sealant and fasteners. There was a slight curvature on the ports, which fit the hull very well.