A few stray thoughts:
The VF-1 doesn't carry fuel, exactly, but it does use reaction mass while flying in space. From a control management standpoint it could behave the same way.
The keypad on the right side panel reminds me of a KNS-660 FMS (which I've actually used) or the ICP on an F-16 (which I've only seen pictures of). I'd imagine it's alphanumeric, like the keypad on a phone, and can be used for data entry in any system, controlled by a rotary switch or selector buttons or something.
The screen directly below the primary flight display looks like an FMS display. Alternatively, since there don't seem to be any standby flight instruments on the panel, that screen could fill that function.
I'd imagine the most practical approach would be to come up with a list of controls that you'd need to operate an aircraft like the Valkyrie, and then start installing them on the panel. Keep in mind that systems tend to be grouped together. All of the lights will be next to each other. All of the radio controls will be next to each other, and so on. Since the VF-1 is a nuclear powered aerospacecraft, it won't be exactly the same as a modern aircraft, but will still have some analogous controls. One example I can think of is firewall shutoff valves and fire extinguishers. You could instead have "Emergency Reactor Shutdown" handles or similar.