After more trial and error and doing more research I was able to get a second server setup on my server's D: drive. I simply copied the game folder over, adjusted the .bat file for the secondary server name, and ports. I was also able to manually add a mod to test. It seems to be working as I can have both servers running art the same time, one with vanilla, and one with Valheim plus on it.

Now I am having a problem with my PC client not being compatible with one or the other depending on if I have the mod installed or not. Is this where a Mod Manager would automatically select the correct mods for a specific server's mod list?

I dont want to have the manually add and remove the mods from my client each time I move from one server to the next.