It sounds like you may have a limb length discrepency but its had to say 100% without an assessment. What type of surfaces do you run on? try and alter your routes as the pavements have a slght camber and that may have made an artifical limb length. Have you had a full biomechanical assessment? If you have not let me know where in the country you are and I can try and get you some contacts. re your blisters buy some white non stretch zinc oxide tape, a couple of pound from the chemist and put a large stripe over the blister area with out any creases usualy best to do this as soon as you feel a hot spot developing but if the blister has formed it should still help, as it sounds like your shoes are rubbing so maybe slightly over pronating. This is probably not want you want to hear but you should stop running if there is pain as you may make it worse, rest, ice, stretch etc, let me know how you get on.
Tell me abit more about your injury, Im just new to running this year but I am a podiatrist as well so I can try and help. Do you wear orthoses/insoles at the moment? As you are wearing a neutral shoe or do you have high arched feet?