Could upper body aching (shoulder, neck, upper back, collar bone, chest muscles) be caused by repeatedly laying/sitting awkwardly as I know I do this?

Perhaps but more. This needs to be clarified as to whether there are other medical issues that could be causing the symptoms. This type of widespread discomfort we see in Fibromyalgia but there may be mechanical issues or other things I need to be considered. You need to see your physician to get clarification.