Hi Rob

I think Dr.rana is jumping to a conclusion before knowing what is going on. In fact this could be due to a number of things that may not be musculoskeletal in nature, which is really NOT the realm of knowledge of a physio. making nutritional recommendations while can be very sound are not part of the cope of practice of a physio. I would therefore would be not want to provide a "diagnosis" or advice based on what you have written. However if you came to me as a physio my thinking would be:

These are quite extensive symptoms - three major muscle groups at least

You are young and presumably very fit so you shouldn't be having extensive symptoms like this so early into your training - I take it you are not very far into your level of exercise before you are getting symptoms.

I would see the Dr and get a good medical workup and thereby rule out other diseases before seeking a musculoskeletal diagnosis.

Muscle tightness can give you aches and pains but you should be really well warmed up by 3 miles so I think it is unlikely be due to that. However if you've been checked out medically and all seems well then a detailed musculoskeletal assessment that includes examining your running on a treadmill is a good way to go - it is possble you are getting some sort of overuse problems but a proper biomechanical assessment is needed. Again I think you need to be assessed properly and not rely on advice on the internet. If you went to your Dr would you not be able to get physio that way?

In the mean time I suggest you avoid running as your main aerobic activity - certainly stop short of the symptoms.