Hi Steve
I'm not sure I fully follow how you intend to use dowels but I'm sure what you are suggesting will work as long as the pine unit is a comfortable height and sturdy enough not to wobble.
I would just keep it simple for your first mirror. Some screwed in cleats covered with a few layers of newspaper will work. Just discard the newspaper between grits. That will do a lot of the cleaning for you. I recommend formply as the base for your top. You get it from Bunnings. It's a plywood used for working with concrete and has a thin phenolic resin coating on both sides. It's easy to clean and you won't need to coat it. It's also cheap.
After you've made a mirror you will develop ideas about how you want to work in future. For example a motorised turntable running at 3 to 5 rpm is easy to build and makes the process easier.
If you want to make a top that can handle different sized mirrors then you could get some ideas from reading P34-39 of this manual:
http://mirror-o-matic.com/conversion...conversion.pdf
Hope that helps,
Rod.