I don't see anything wrong with your setup, although I would probably do it differently.
2. This is an odd one. If I open JRiver with my 1440p monitor set as the primary, it only shows resolutions from my first monitor, not the second
I think this #2 is probably at the core of the issue.
As for what I might do differently, you could try disabling mode switching inside MadVR, and let MC do the mode switching. This is generally more reliable, I find. But based on #2, I'm doubt that it would do any good in your case.
What you see in #2 is that MC is seeing only certain resolutions, and not the correct ones. Whether this is a Windows/driver problem, or an MC problem, only Hendrik could say. But as long as MC cannot see the correct resolutions for the monitor, there are going to be issues.
The only other idea I have is to play with one of the settings in the Compatibility tab for the MC application. There is an option called "Override high DPI scaling behavior" and perhaps one of the settings there could improve this. And perhaps it it might have a different effect it if you combined this with letting MC set the display mode, as I described above.
Good luck.