Running is actually very hard on your body mechanically. I used to be a long distance runner (even did rather well in competitions in high school); I loved running. Now, however, I can see the wear and tear it put on my body, especially my knees. Running in moderation (like anything else) is manageable, but extensive running is problematic. Lower impact exercises that challenge you aerobically, such as swimming, elliptical machines, cycling...hell, even a good, brisk walk...are better for you in the long run.
As for ruck marching, I'd offer the following suggestions:
-consider carefully how you arrange your load. As a sect comd and later a pl comd, I tended to check my soldiers' loads pretty carefully, and as a coy comd and CO, I did occasional "spot audits" of my soldiers...in many cases, their loads weren't well balanced. You want to keep as much weight as possible close to your centre of gravity, which is generally around your belt buckle. You also want to ensure you use a hip belt, to place as much weight as possible on the strong bones of your pelvis and legs. Weight transmitted through the shoulders requires much more muscular effort to carry and balance, which is more fatiguing than simply allowing a static transfer of forces through the bones of your lower body
-needless to say, you want to carry as LITTLE as possible. It may go without saying, but I've occasionally had soldiers carry the most wonderfully bizzare stuff...like extra cans of shaving cream "in case they ran out", or a six-pack of pop in the bottom of their ruck "for when they got tired of water". You need to carry a) what you're ordered to carry, then b) what you otherwise need to live and fight in the field...and that's it.
-take care of your feet. There are other threads on this, so I won't belabour the details...the point is that if your feet are bothering you because of blisters, etc. it will affect the way you walk, which will affect your balance and the distribution of forces through your body, and again, increase fatigue. And if your sect or pl comd wants you to take off your boots so he can inspect your socks and feet, don't look at him likes he's some sort of pervert...it's called taking care of your soldiers. I wish more junior leaders would do this sort of thing.
-hydrate. Another "motherhood" statement, but again, inadequate hydration affects your body chemistry, which again translates into things like the extent to which your body can flush away fatigue toxins like lactic acid from working muscles. The same goes for overall nutrition, particularly including things like electrolytes (be wary of bottled water, as it contains very few dissolved minerals; your body requires certain ionic compounds, like salts of sodium and potassium, for normal neuro-muscular function)
-finally, mental toughness has been mentioned. Yup, this is probably most critical, and the hardest to develop. I find that minds tend to shut down long before bodies do; rare is the soldier who literally drives himself until his body gives up (though they do exist). Ruck marches are, generally, BORING...a bored mind is idle, and idle minds will almost always find a way to entertain themselves, even if it's just to explore how miserable they are. You need to perform mental exercises while you march. Count things, play tactical decision games with yourself ("if a sniper fired at me from that window, what would I do? where would I go? what sort of fire position would I take up? what message, exactly, would I relay to my section? Okay, what if an MG fired at me from that tree-line...?"), talk to buddies (if you're able and allowed to), make up stories in your head about people you see ("that guy over there...what if he's a terrorist? Where did he come from, and what's he planning?")...anything to keep your mind engaged. This presupposes, of course, that you're on an administrative ruck march and aren't moving tactically, in which case your mind should be engaged with keeping yourself situationally aware (which you can do anyway, as another mental exercise)
