Just a few more ideas on kicking a side ache. I've been experimenting on myself as I've been getting back in shape. My calories are at a healthy low, which means I'm losing a bit of weight and also getting LOTS of side aches when I run. For me the two just go hand in hand. A few things that have helped me run through the pain are 1: making sure my tail bone is tucked under. A lot of runners will start to push their chest out/ache their back as they become more fatigued (myself included). When I do this I notice the pain more, but when I think about running with my legs instead of my chest and keeping my booty tucked in, it seems to help.
2: INCLINE. Have I shared the secret on incline? I once talked with a nutrition guru and he told me that to get someone over a platue turn up the incline. You can crawl, walk, or run, but get that treadmill turned all the way up to 10% incline! I've also found this helpful when kicking a side ache. I usually run at a 2% incline on a treadmill, but turning it up even more for a few laps helps when pain comes.
3: GO FASTER. I've been sprinting through the aches too. Although it seems like the last thing you'd want to do, it relieves some of the pain I have and also makes going back to a normal pace seem like heaven.