First things first.
The "mag" part. You got 1p and 3p correct, and the third, the "weapon" animation is simply everything that moves around the weapon, which usually consists of multiple parts (well, mostly the "base" and a "mag"). Animating those is done in a separate .baf.
Animating the weapon itself works just like the rest, no need to delete anything, that wouldn't make sense. The mag in the russsoldier does not disappear, it is just moved out of the field of view of the player and then returned (the same one!). As there's no visual difference between a full and an empty mag. Anything that you want to "disappear" during an 1p animation, just move it out of the field of view.
EDIT: Check this video:
http://www.youtube.com/watch?v=sVEI4hg9 ... tube_gdata - First half shows the animation as seen by the player ingame, second part shows how I did it. The removed mag never actually is removed, I just moved it "away". The small cylinder in front is an indicator I placed so I know where the ingame crosshair is, so I can adjust my animations accordingly, making the weapon point roughly towards it. Also, I regularly make the soldier's head invisible as well as the body "see-through". Helps a great deal when animating hand details. And sorry for the texture fault, I quickly rendered the vid on max11 where the BF shaders don't work, my max7 still is acting up.
Oh, there's another limitation: No weapon animations in 3p possible. So in 3p you can never get the magazine to be shown separated from the weapon. A pity, but that's how it is.
For your Owen, you'd need to make all animations all over again. My tip: Start with a good max saving structure and save a individual .max for every single animation. That means a lot of .max, but will be worth it once you have to make various adaptions...also, name the .max very clearly. My structure: Folder name=Weapon name. max name: 3pSoldierCrouchBreath etc. . Exactly like the animation name.
I'd suggest starting with the basic and most important animations. These are "Run", "Walk", "Crouch", "Lie", "Stand". Best is to start with "stand" obviously, as most animations will transition from there. Transitioning between animations is done by Refractor, it simply interpolates between the "current frame" to the "start frame" of the new animation if triggered. Obviously, this transition should be done very quickly and as smoothly as possible so it doesn't look all weird. So especially Stand and Run should be well animated.
To get your weapon in properly, there's a small trick that can be useful: Import the skeleton of your weapon first, in a separate skeleton.max. Then you get a bunch of ugly small boxes that have the perfect position (if you have implemented the weapon already). Write down or remember how every weapon part is called (Case-sensitive!). Then import your weapon standardmeshes in a new weapon.max. Name each weapon part exactly as the skeleton parts. Then switch back to skeleton.max. Now you can just replace the boxes with your weapon parts via File-Replace. Then import the weapon to your russsoldier-base template and it should be attached to Bip01R. If not, do it yourself (Link constraint, you probably know the deal).
Once your soldier and weapon are in, I advise starting by importing a basic "existing animation. First import the regular "Run" animation for the Lower Body. Yes. That is because all upper body animations are based on the lower body-run animation. Don't import "Lower Body stand". A standing soldier is obviously a bit taller, yes, but even the Upper Body "Stand" animation accounts for the lower body to be running. Confusing, but that's how it is.
After you imported the Run-animation, there should be all "changed" bones selected automatically in max. Now delete all frames except the first to prevent your soldier from bobbling up and down during your animation code. As said, run animation is the base, but only the first frame as a "fixed stance".
For 3p-animation, you need to account for lower body animations, obviously, but we currently talk 1p.
After that, import the best fitting animation for the upper body (1p!!!). In your case, maybe the Thompson one. You can try around here. There will be things off, but you get a basic animation of the upper body moving during running and thus a bit of "feel" on how your final animation should look like. You even can leave all the upper body untouched and only alter the "important" things: Attaching the hands to the gun correctly and the weapon "swaying".
Once you have your first animation all done, it gets easier, as you can use that base (as said: "Stand" animation works best) for every other animation of that weapon. That will save you a lot of hazzle.
EDIT: Included video link for the how-to-exchange-mag? issue.
Also, a hint regarding animation of the arms and hands. Us a Animation-IK Constraint to link the hand to the shoulder on each arm. Before you fiddled with the imported animation. This has the HUGE advantage that you only need to move the Bip01R/Bip01L and both arm segments will move "fittingly" as the IK Constraint dictates them to interpolate any movements of the hand. This avoids you having to place any concern on the arm movements.