Finally I managed a way to get rid of the full brights. It took quiet some time before I realized how to manage this. After resizing the skinfiles so they were divided by 16 I could import them into a wad.
Then in Texmex make them fullbright and delete them.

Still some monsters have a strange red shape, also the skin tex is flattened. But most fullbrights are deleted now.

Still I wonder how to get the Doom Guy in a crouch scene. If I lower the bouncing box the model also sinks in the ground (?!) 

i've found a (possibly better way) of removing full brights.

i've been doing some skinning and texture work lately for quake, and dealing with the palette kinda sucks especially because things like texmex don't have great conversion.

the solution is (amusingly) pretty simple. get one of those palette textures that has every colour of the quake palette and load it in photoshop. now, simply remove the first two rows (at the top) of colour boxes because those are the fullbright ones.
convert to index from rgb (or if it's already in index, convert to rgb then back to index) and choose 'exact'. now, you can open up the colour table and save the new palette. this way you can use photoshop's nicer dithering choices.

this also works in reverse. say you are converting an explosion sprite. do the above, but instead delete everything except the second from-the-top row (these are the full bright colours used for flames and such) and do your index conversion with dithering. you'll get a decent conversion with only those fullbrights.

this might be a well known thing for you guys who do textures a lot, but it's saved me a ton of time since i figured it out. 

Is now my final stage for a model, basically just to set the correct flags. But one feature it does have is colour replace - you can replace all instances of any given colour in a model for another.

Goodbye fullbrights - which are the bottom two rows in this zany old software. 

since they are color indices 224-255 

and display the palette backwards, going from 255-0. 

the .tga file i have of the quake palette has the vertical flipped, i believe. anyway, you can easily figure out which rows are the fullbrights because it's pretty evident. :)