then you dont have to convert to md5.
just replace them...

Yes I do!
The Trooper edition gun models are in md5 format, the CTF edition ones are in md3 format... when I put the CTF 'hudguns' folder into Trooper edition, I just keep the old models. I think it's a redirect thing... is there a way to convert the file format?

there are 2 files of hudguns that should be replaced, to get it (as far as i know).
the first is just in the "models" folder with the name "hudguns" (just out of my head, im not on my own computer right now :S) and the 2nd is in the "mr.fixit" folder, with the name "hudguns" too. if your using ironsnout10k, then replace the folder called "hudguns" into "snoutx10k" too...
btw, just use the "hudguns" folder of ctf edition, not "vwep" or anything else!

btw, if replacing doesnt work, delete the original folder firsts, then paste to folder you want to (but always make sure you got a backup of the original folder!).

there are another ways for this, by changing paths to textures, md5's and md3's even tough its harder (but more proffesional :P).

gl and hf.