Mark - the best advice I can give you is to see a physio. Pain that is worse first thing in the morning is "normal" with injuries - things stiffen up over night whilst you are not moving around and ease off (speaking from experience! often in the shower) as you begin to move around the next day and loosen up.
You seem to have a number of problems which could be a lot of issues but probably all related. You need to find out the root cause of the injury - referred pain can make it difficult to pinpoint exactly where the problem starts. For example - lower back pain is not necessarily pain due to injury to the lowerback but can be caused by lots of things - tight glutes/weak core/piriformis problems. Knee pain can often be caused by ITB problems - again ITB can be caused by many different factors.
Your thigh pain does need investigating - its getting worse though you are not running. If you cannot see a sports physio - see your GP. Explain the whole story - not just the worst pain you have at that moment! All your sore bits are relevent to a successful diagnosis.
Good luck - I hope you get answers!