The only place that you are going to find the HVHP gears are from S&S. The shaft is the same as is the seal, keys and clips. There should be a two or three letter code stamped into the side of the case above the oil pump. There is a chart in the catalog that you can match that code to to determine which bolt/passage pattern you need for your pump and gasket. Whatever you do, do not use stock HD gaskets with that HVHP pump. It actually uses a gap in the gasket to move some of the oil. A stock gasklet will block the flow. The cover should allow you to run the feed and return lines however will work best for your application. As far as breathing goes, You can set that motor up to be either a top breather, bottom breather or both. It is going to depend on whether your cam cover has the passage into the bottom breathing chamber or not. If you choose to use the bottom, use both of the passages. Which heads do you have? If you have the correct heads for the 4 1/8" bore motors, I would use the breathers built into the heads. It is a much better system.
I almost forgot. With that motor you need to run the HVHP pump. There are piston oilers like a twincam that need the extra oil volume of the HVHP pump. That's actually why the pump was introduced.