I just ran into this issue doing my Future mod, and got help with it, and it took me about a week, and in the end I got something that works. There is a tutorial about part of this task, but pertains to photoshop and doesn't cover all aspects. I have Gimp 2.2 with a tga plug in that I downloaded. I took the res/fonts and res/fonts75 from the thomas' war mod since it uses all the slots. Then I copied and pasted replacement stuff right over it. Pasting into an existing one over an existing icon works much better than trying to put them into position by eyeballing. You have to be very carefull about exactly how you cut and paste, because this file is very sensitive. If you have too many icons it will offset everything by a position or a line, kind of unpredictably. If you have any stray marks it will read them as icons. Once you think you have it you might want to check, because for the longest time I had an issue with happy faces and unhealthy icons showing up in the wrong places.
Also, the religions and corporations will be given icons based on order in the xml files, so the first religion gets the first two icons on the religion icon line in the font atlas, the second religion gets the next two and so forth, then the corporations.
There are also issues with different channels or something with tga, so you are better off trying not to copy stuff into the files from other formats. Either copy something from another tga or paint it yourself. And of course your regular dds buttons also have to be done, but they are relatively straightforward.
As for a new opening screen, CIV4MainMenuBG is a nif that handles that. You can find its placement, (Assets/Art/Interface/Main Menu/) then replicate it in your mod. Then supply a substitute dds for it in the same folder and if you have renamed it use nifscope to make it use that dds.
You can replace the dds
LoadingScreenBGBeyondtheSword
in Assets/Art/Screens/Loading/ with another dds that has the same name and that will give you a second screen for while the mod is loading, as well as for behind the main menu.
