Yeah, when the EVA cushioning goes, it tends to compress into a sort of rippled effect, but you can also feel it when you run - everything will be sort of thuddy, especially on hard surfaces.
For stretching, take a look at the Bob Anderson book, 'Stretching' which is pretty comprehensive, but one thing you could try if you have access to a pull-up bar and your shoulders are sore rather then actually injured, is simply to hang from the bar on straight arms for between 10 seconds and one minute. You'll get a gentle stretch right down your body. As Alex says, chances are that it's not just your shoulders that are tight, so what you really need to do is look at an overall stretching routine for your whole body.
