Weapon animation is controlled by _hand.md3 (machinegun_hand.md3, shotgun_hand.md3, etc). This model controls where the gun is placed in first person, and also has the animation for the gun dropping/raising, and firing.

Frames 1,2,3,4,5,6,7 are the guns firing animation, and frames 8,9,10,11,12,13,14,15,16 are the frames for dropping and raising. What you want for frames 8-16, is the guns rest position at both 8 and 16, and the guns lowest point when dropping to be at frame 12.

To animate it, just add a single bone to the gun model, with the tags parented to the bone, and export the bone with the tags, but not the gun model itself, for _hand.

Example:

Machinegun.md3 is just the gun mesh, and the tags, with no animation data, and no bone exported.

Machinegun_hand.md3 is the tags and the bone, WITHOUT the machinegun mesh in the file. So all that is in this md3 for machinegun_hand would be tag_weapon, tag_barrel, tag_flash and the bone. You want to export both models the same scale, but for _hand.md3, you can offset the x/y/z to whatever you want, to move the gun in the first person camera. The easiest way to figure out what offsets you want, is to load the game up with cheats enabled, and change cg_gunx, cg_guny and cg_gunz until you find a position you like. Then when you export, those numbers you used for x,y,z, you can use as the same numbers for exporting _hand.md3, in the offset fields.