Why doesn't someone do this:
Open one of the original fpsc guns in milkshape.
Utilizing the "MERGE" option, merge your new gun model with the fpsc one.
Once you have your gun rotated and in the same position as the fpsc one, delete the fpsc one.
You can then animate it or use the fpsc one's animations, and don't forget to add the bones for the firespots
Then export it and duplicate a folder of the gun that you used as a template.
Delete the gun model in the duplicate folder and put your gun model in. Make sure you use the same name for the file as the file you deleted. You may rename it right there, no need to re-export.
Change out the textures in the folder with your textures
Re-name the folder to the name of your gun
And you are done.
***BONUS***
If you were smart, and used the default gun's animations, there is no need to edit the animations at the base of the gunspec. However, if you did, go back in milkshape and get the appropriate frames. Need to know what animation numbers are what? Open back up the default gun in milkshape (save yours first) and let the animation loop. Watch the frame numbers and read the default gun's gunspec, and read through to figure out which frames correspond to what. Then you need to change those frame numbers to the right ones and you are good to go.