Since you know the whole modeling thing the next part is getting them in engine.
I have always imported a D3 weapon that is already similar and would use it's skeleton structure as a base. If you use the same bone/animation names then it's almost as simple as just making new animations with the exact same names/locations as the stock ones. I use Blender to do my modeling/animations, not sure what you used. Motorsep released md5 exporters for more modern versions of Blender. They should be in the sticky thread in the models & anim section.
The appropriate forum for this is the models & animations section so I'll move it there. But peruse through that for some help too:
http://idtechforums.fuzzylogicinc.com/index.php?board=36.0