New shoes shouldn't give blisters - it sounds like the support is in the wrong place for the arch of your foot. This happened once when I was advised to wear Asics shoes that just didn't suit my feet. I went back to the shop and they exchanged my shoes for another make and model.
I'm no expert and I don't know how far you run from scratch but I would suggest getting a good fitting pair of running trainers and to build up gradually. Try to walk for a few hundred metres to warm up before running and take frequent walk breaks until your body is more used to the stresses of running.
I'm not sure that running through pain is always the best cure. If you do get sore legs from running then maybe you could walk the distance instead until the pain recedes?
It's a question of trying and seeing what works best for you. I have a rule of thumb that says 1 hour between eating and running for distances up to 20km and then 2 hours for longer than that. But I have got here by trial and uncomfortable error. But an hour is probably a fair bet.