So during my time in Japan I was able to pick up a Naomi and Atomiswave, unfortunately the former is incomplete. But anyway I really want to play my games. Although I don’t know if modders are around as much anymore for consolization, and I’m a little iffy with shipping my mobos now that I think about it. So the next best step is to do a supergun with Undamned USB ports and/or Saturn ports.
I also want to be able to do VGA+RCA to HDMI like this guy didin the YouTube video below, but I got no reply back when I asked. Remember, Both of these can output native 480p. Yes I know not all screens can take 480p in that frequency.
I have other custom supergun questions like is it possible to do four ports (2 UD and 2 Saturn), but they act like 1P-2P on one setting (so you can choose between Modern and Saturn) and on a second setting each port is set from 1P-4P, because you know Power Stone 2 or if I somehow get a CPS2 and decide to play 4player D&D or 3player AvP. Though for video it would be something else since the most CPS2 can do is RGB so I would need an upscale like the OSSC to get that on a modern screen without problems. But a PVM is a better option for older stuff. EDIT: I’m totally overthinking this for UD and Saturn support, looking at arcade projects, the HAS supergun can basically do what I was asking. Lol I think I should just go for that, unless you got suggestions.
I am aware of arcade projects, when I am ready to buy I guess I’ll ask there. But I wanted some more advice first. Lol
Pretty loaded post. 
But pretty easily answered.
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In regards to VGA+RCA to HDMI: you’ll just need a some sort of analog-to-digital converter, even though the Naomi/Atomiswave can do 480p. The catch is finding a well-priced one that doesn’t add a ton of processing to it. As a Naomi owner myself, my question to you is: Do you really need the HDMI? Naomi plays just fine on VGA, and I’ve very often hooked up my Naomi via VGA to a screen, and then connected the RCA output to an external set of speakers.
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In regards to your controller port dilemma: yes, it’s possible to do P1/P2 (UD-USB/Saturn), and have them switch to to P1/P2/P3/P4. It’ll just involve a ton of wiring and switching because, for just one port, you’d be switching 12-15 wires from one set of contacts (P1-Saturn, for example, but leaving P1-USB intact) to a whole different set of contacts (P3, in this same example). Personally, I feel this is something you’d definitely want to map out on paper before doing the actual work, and you’re probably better off doing this via a custom switching PCB as I don’t think it’s practical to do this via physical switches (though a Google Images search returned a 36pdt switch that’s useful in this case, but probably super-expensive).
Does Naomi/Atomiswave have VGA out already and takes an ATX Power Supply? Wouldn’t a VGA to HDMI passthrough work out well? I mean, I’m actually for composite output for older consoles since transparent meshes being dots instead of transparent hurts my eyes, but Naomi shouldn’t be an issue.