Basically I want to strip out the unnecessary stuff on the 2d map and make it more clear. For example, number every single building and barrier, highlight important points, backalleys, and hiding spots. I'm pretty sure it wouldn't be considered illegal, but I have a feeling it would just automatically 'fix' itself everytime you joined a server. I can explain it better if you need me to.

Use gcfscape to get the proper minimaps textures out of the gcf file, convert it to a tga file using vtf2tga. Once that's done you can edit it with Photoshop or a similar program, then convert it to a texture and place it in the same directory on your drive as the one the original texture was in the gcf file. Everytime you run dod, the new one will overrule the gcf one.

Is it possible to do this with standard dod maps (donner, avalanche, jagd, etc) or only with custom ones?

edit: Nevermind I found the .gcf file, sorry :( (i was looking in the wrong place)

It worked perfectly, thanks!

be aware that this might not work for many customs. Most custom maps, unlike the stock maps, have the minimap packed into the bsp. The game looks for the map there first, before checking your dod folder, so it will always display the intended map, and not your editted one.