Honestly stretching before running does little to nothing for you. The reason is because your body isn't warmed up and it's simply not doing anything for you at that. You can do a little bit for your hips, calfs, quads etc... to help the process but it doesn't do anything for your side cramps.
As for your side's hurting, you need to drink more water. You should be peeing clear about 20-30 min before you run. Aside from that it's a progression thing with running, if you don't stay on top of it you will always cramp in those areas because your cardio will lack in comparison to the amount of running you are trying to do. The first week or so you will have cramps but as long as you run on a consistent 4-5 day trend after that it will go away naturally. Also for eating, it's different with everyone. If you are noticing cramps it probably means you should wait about an hour or so before running.
Lastly after running make sure you spend 15-20 minutes stretching and around 10-20 minutes of icing on your joints/muscles to prevent injury. Personally, I'd just do an ice bath for around 6-8 minutes and that will do the job but its cold let me tell ya.
That's about all I can give to ya for now, message me if you have anymore questions! Humbly put I do run in college so I have gained a lot of knowledge over the years from running. =D