From what I know, IQM was technically meant to replace MD5.
http://sauerbraten.org/iqm/You can also have a look at the model reference.
http://sauerbraten.org/docs/models.htmlYou can also look at the old hudguns' md5.cfg files and see how the model is set up from there.
Noesis is a good tool to have in the matter of models. You can export one of the md5 hudguns as obj and look at the models in Blender to get the idea of what they're positioned and scaled to, although you'll still need a proper configuration file for it.
http://richwhitehouse.com/index.php?content=inc_projects.phpOne thing I will mention if you intend to replace something. Make sure you rename the old config file to something else like md5_copy.cfg or something, just anything but md5.cfg. Otherwise, the game will STILL use it even if you use a different format like md3.cfg.