I used experimentation, assumptions on how things work, basic Blender knowledge, and help on that board, but I can help you on some points:
1.I use Blender, a MDL importer, a MD3 exporter plugin, Preach's MD3 to MDL converter tool and QME to properly save the mesh's texture and check if the actual model is Quake-compatible and see if the initial result in Blender is very close in here.
2.For scale references, import quake models from the actual pak files.
3.Do low-poly meshes. Import more quake models if you want references or look for low-poly tutorials.
4.Mark Seems properly depending on the mesh's elements, so texturing is comfortable. You can then organize them better by splitting the image in two and manipulating the UVs here. Don't forget to snap them to pixels.
5.Do texturing in Photoshop or Gimp. I used photoshop, I always start with a 216*216 resolution, and used various Blending options while taking colors from the quake palette, and noise filter to make things more grainy. I go back and forth between Photoshop and Blender to see if the texture's elements are placed right (Use "Reload Image" option in the UV editor). When it's done, I scale down back to 200*200, darken the texture to fit into quake's lighting if necessary, and apply the Quake texture on it. Final exture must be a pcx file with the quake palette applied on.
6.Apply the texture as a Material. Preach made a post about this earlier.
7.MD3 export, MDL convert, QME check/texture save.
For animations, you have to use Shape Keys. It works like this:
https://www.youtube.com/watch?v=ecAHLfp9Nw8
To apply them as actual frames, you have to use the Dope Sheet editor type, where you apply the percentages of the keyframes and register them as frames. It works like the TimeLine, so frames are made consecutivally.
Hope that helped.