When doing the setup I chose the direct 3d renderer, any attempt to run the game in full screen results in the game staying at a very small window resolution in windowed mode. The only options for resolutions are all smaller than 1000 in any dimension

What do I need to do in order to run the game at a decent resolution?



Edit:
I found a way to increase my resolution, however I am still getting unusual visual bugs and low frame-rate. What is the best way I can handle these? Also is there a guide anywhere for how to set up various recommended mods and fixes?

Yeah the default D3D renderer for UT99 was for DirectX 7 so you would be best to use a newer renderer

You can get d3d9 and opengl renderers from here that will work much better.
http://www.cwdohnal.com/utglr/

Here is a tutorial on customising the graphics settings for UT99 (haven't used it myself but it looks to have everything)
https://ut99.org/viewtopic.php?f=6&t=373

Also D3D10 can be found here
http://www.kentie.net/article/d3d10drv/

GoG version is a total mess.