I'm not sure what you're worried about for the long term. My HS and other emp parts have been hanging in storage in my garage shop for several years and are as shiny and pretty as the day I pulled the rest of the blue vinyl off. This is common. I think if you have a reasonable shop environment, you have nothing to worry about.
I'm no expert when it comes to paint. There are others here who are more knowledgeable than I am, but I do understand that most exterior aircraft paints are applied as a 2-part system. That is, a primer that is specifically designed and formulated to bond with the topcoat for a strong long-lasting paint job. There's a lot of chemistry involved here. There's also a time factor, between when the primer is applied and the optimum time to spray the topcoat. Bottom line is, you don't want to use just any primer with any topcoat. And I don't think you want it sitting around a long time after priming before it's painted. So if you spray your stuff with Mar-Hyde now, my strong hunch is you'll be stripping it off later on in order to apply the proper primer designed to match whatever topcoat will be applied. If I were you, I'd hang my parts up in storage and build on.