I took a couple weeks of rest after the last 5k I ran. It did a number on my shins as I didn't train as well on the pavement as I needed to. Running on the treadmill doesn't hurt my shins - pavement does. I'm still keeping my stamina/endurance up so I can still run the distance, but I guess it's time to get back to training again. The plan is to train the rest of the summer, run a 5k in the late summer, try a 10k somewhere, and then run a half marathon in November. I think I can do it. No wait, I know I can do it. I doubted that I could run a 5k and proved myself wrong. Back in March when I was training, I essentially was running a 10k distance, so I know I can reach that mark within a couple months.
Injuries have a funny effect on you - they psych you out. I run expecting an injury now, when before I ran carefree. I guess I need to find a space in between mentally.
There were a few things I did to overcome similar pain, you already seem to be doing all of these. A doctor also told me not to run and just walk - I simply refused to be limited.
1. Shoes, regardless of brand I had myself fitted at a two running store that had a 30 day return policy. This allowed me to try four different brands & model of shoes in my real world, not just the store's. I finally settled on two different pairs.
2. Stretching/Warming up before each run.
3. Running form, Stay light on the feet. I keep reminding myself of the running form to maintain.
I did a half marathon on my own and have done 5K and 10Ks in organized events. No problem after the run as long as I stick with points 1, 2 and 3.