About the gudgeons (or pintles - whichever attach to the rudder on your boat) I would recommend through bolting them with high quality SS (stainless steel) nuts & bolts (#316 or close). For the hole that goes through the wood you should check out MaineSail's 'how to backfill a deck hole' help page and substitute his fiberglass for your wooden rudder. Then drill your hole for the bolt.
Sealing Deck Penetrations to Prevent Core Rot Photo Gallery by Maine Sailing at pbase.com
West System epoxy even has a graphite powder you can add that might not be a bad thickener for bedding a hole for a SS screw. In any case I would drill a slightly oversized hole through the wood and fill it with thickened epoxy as outlined in the link above.
Since you are going to be a trailer sailor you can get away with sailing on bare gel coat (as probably is) with a rinse every dip. You shouldn't need toxic and expensive 'anti-fouling' paint unless you plan on keeping your boat in salt water for more than a month or two; freshwater is a bit different where slime and algae can build up more then barnacles among other growth do in salt water.
If you are not going to use any kind of fiberglass cloth in the layup of your rudder I would advise you to consult the West Systems website for their recommendation on this application. I would use some of the Colloidal Silica (#406?) and/or their fairing compound (#410?) for the surfaces.
You probably don't need to use fiberglass cloth to enclose your wooden rudder with. The final argument for doing so is that the cloth adds quite a lot more strength to the epoxy bond and should your wooden rudder ever split along a grain the epoxy/cloth layer has a chance of holding it together for a short while (laminates = strength).
"I will put a solid 2 part epoxy paint on it though."
This is probably a good idea but it does not need to be an 'anti-fouling' paint, just a hard epoxy paint (white works good for the hull - it shows all the dings you'll want to repair and paint).