If you want to make a more versatile control panel, it's probably not that hard to remove the existing control panel without damaging it or the machine. Once you've got that off, you can design your panel to attach to the cabinet in the same way, and if it needs additional support, you work within the area covered by the original panel. Then you can transplant whatever controls you like from the old panel to the new, or go with all-new controls.
Beyond that, cosmetically, all you really have to/can do is change the marquee. There's plenty of room inside most 80's cabinets, so you can mount whatever PC components you need without having to disturb the original board setup. Just reroute the sound and video however you plan to do that, and you're good to go. So now, when you want to go back, all you have to do to get it looking right again is switch out the control panel and marquee. Then you yank your extra stuff from inside, and plug the old connections back up.
I wasn't so tender with the old Phoenix cab I used. It had been through multiple violent conversions over the years; a plywood box inside made for a vertical-to-horizontal monitor kludge, several half-inch holes had been drilled straight through the side panels, side-art was long gone but the adhesive wasn't quite, etc. I did try not to make it worse, but it's not as though it was a pristine Phoenix when I started. Now, I have an old Super Cobra that's all original; it's a bit beat up, but all it would take to make it look sweet is some fresh t-molding and paint (Stern cabinet's an easy stencil). I need to sell it before we move, but I fear for its fate.