Ah well, you live and learn. I like to think (and weather or not this is true is another matter) if my stitches are as a result of fatigue, then by running to the point of a stitch, I should-in theory- be building up the muscles which will in time keep the stitches away (core muscles).
That is though as long as your running with a decent technique and good posture using your core muscles.
Stitches can come on for many reasons, electrolyte inbalances is one (as Jason has explained above) try drinking a sports drink or orange juice diluted 50/50 with water which will rebalance your electrolytes and help if that is the issue.
Posture can be another reason, especially if it's a shoulder stitch. Work on making sure your back is straight, hips are inline, knees are below your body and not running ahead of it. Then make sure your upper body is relaxed as tension can create cramps. It can take a while to get used to running without cramping up.
Fatigue though is another big reason. The key to this is keeping tabs on how you feel and stopping yourself before the stitch becomes a stitch -you do get subtle warning signs. If you feel a stitch coming on, slow down and stop, stretch a little, don't totally cool down but get yourself to a position where the to-be-stitch feels pretty much gone, then go back to running. Once you have a stitch your on a losing streak as to trying to get rid of it as it sort of leaves a mental mark behind so even when it is gone, your posture has already altered to expect it to come back. Doing this can end up with a stitch elsewhere (eg shoulder!) and then you get nowhere fast.
I took a sports massage, as I didn't have a diagnosis (first Physio decided that without a proper scan, I was just making a fuss over nothing and needed to hop and carry on hopping to get used to the pain). The spots massage person said I had to stop running. I had been told to carry on by the physio but took the advice (which was not easy to understand because cycling and using a cross trainer hurt just as much as running but I did stop).
6 months later it had stopped hurting and I was able to run again- all be it on a treadmill. Then I changed my running, went outside and it came back pretty mushc straight away. I was gutted. I then managed to fall and sprain my ankle....
Luckily I was seeing a private physio for the new leg pain- having taken the advice of the sports massage student I'd seen who told me if it came back, to see a GP and get proper help- I had luckily been referred to a private physio and I was very amazed at how good the care was. I was able to see someone 4 times and each time had new strapping applied- properly wrapped do-not-remove type strapping. It really did help. I have learnt why and sadly could not repeat the same results when I tried myself but I really feel of all the things I tried, rest and strapping made the greatest difference.
Rehabilitation exercises also made a different- special exercises to train the muscles which were weaker and meant other muscles had to take over and so became over-worked, leaning to the bones underneath being less protected when I had worked things too hard (makes the origin make sense I suppose) and was told to not run again. I stopped for a total of 6 months (I'd been told 8 months by the orthopedic Doctor I was later referred to- bare in mind I had this pain for over 2 years at that point). I also took up a new style of running where I landed on my forefoot or mid foot rather then my heel thus reducing the impact, reducing the level of work certain muscles were having to do and the pain has not since come back- it'll be 2 years ago in April.
I am not by any means the expert on stress fractures, but I have had one and can explain what my symptoms were.
My leg seemed to be affected after doing donkey kicks (you may wanna google this!) to this day I have no idea why but this is when it happened so I imagined it was a pulled muscle but just hurt in one specific spot- it was a similar sort of ache.
It got worse when I moved my foot to point my toes, or to walk on, or to jump on, or to hop on...it would sort of "pang" with pain on each form of impact -ie when my foot hit the floor or when I got to the end of my toe pointing. Running of course hurt but as much as cycling or just about any other exercise where the muscles in my calf was used.
To explain that, you need to think about how the muscles inside your body all fit together with the rest of the organs and things in your body, when it comes to bones, your muscles are connected with lots of little ties, your bones are covered with a thin sort of covering called facia and when you get a stress fracture, this facia is affected and the muscles which are connected on top are also affected, this moving your muscles can hurt due to the fracture- if that seems a bit confusing, Wikipedia normally has a decent enough description! Am not a scientist so will not profess to be.
It hurt to touch, it hurt to massage and ice did not stop ir hurting- nothing seemed to reach it when massaging- I could easily make it worse by pressing on it, but in terms of stretching it better or massaging it better, nothing had any effect.
I'd normally go with the barefoot/minimalist advice, but it does take some getting used to, and if your new to running, you may want to get the basics right first.
In saying that, I mean make sure your technique is sound, for example your not running with poor posture or you don't have an underlying injury of some sort which would require some sort of treatment or RICE before you can get back to running (slowly). If you do have underlying issues, they will only continue to get worse whatever footwear you try.
But I would advise reading the book Born To Run which is pretty good at explaining how the whole thing works.