For those of you looking for something new to play with the atmosphere of Armada 1, but much better visuals, here is version 4.0 of the Roots Mod, the only Armada 2 or Fleet Operations mod with original single player missons. Version 5.0 of the mod builds on top of Fleet Ops, but has Cardassians, Species 8472, singleplayer missions, and improved visuals, even compared to Fleet Ops. It brings a ton of technical and visual improvements, like larger shell menus, better AI, and better ship movement physics. It also comes with the original Fleet Ops, made compatible with the modified game engine, installed as a submod.

Download link here: https://www.moddb.com/mods/fleet-ops-roots/downloads/fleet-ops-roots-50

This works great, but the menus display in a window and keep me from being able to do anything. I was wondering if there is a way to auto scale the window to fit the monitor or what I can do to fix this. As I can't even change the graphic settings because the "ok" button is cut off below the screen.

You can't auto scale the menus, unfortunately. Fleet Ops menus are hardcoded to be a certain size. If your monitor's resolution is below 1200x900 you won't be able to run the Roots mod properly. If it's above that resolution and the menus still seem to large on the first time of running Roots then you can change the DPI scaling (compatibility tab of the shortcut -> High DPI scaling override -> Override, scaling performed by "Application".