Sebranek, theres lots of problems you could have but you need to give us a little more information.
What kind of food are you eating? (You probably want to take an amino acid supplement) How tall are you? How much do you weigh? Do you have injuries? Are you sick or have you ever been majorly ill??
If running gets you stiff you should start by doing a warm up doing some low impact type of exercise like a eliptical, swimming or shadow boxing. After you are warmed up stretch for a good 5-10 minutes. You can find stretching teq online or ask a trainer at your gym. Most of them are pretty easy, just don't over do it. The more flexible you become the easier it will be for your muscles to move and you won't be so stiff.
Make sure you do like NBS says and always get some rest in there. If you really want to increase your indurance after a running day or two try some boxing. That will wear you out too and is not to hard on your wheels. Ice skating is another idea if that is an option.
Hope this helps you out.