Exercising with a neck and shoulder injury

10 weeks ago I was in a car accident and injured my neck and shoulders/upper back (whiplash). Been going to physio and massage. Slowly but surely getting better. Am anxious to be 100% again though! Have moments of frustration! I've slipped with my diet and unable to do my regular exercise routine, which was circuit training 2-3x a week and running 1-2x a week. A few weeks ago I tried to go back to my circuit training group and followed my restrictions (mainly no upper body, definitely no hands above my head or out front) and overdid it big time!! I was extremely sore for a few days afterwards! I was mainly doing squats, lunges, step-ups. Not only did my neck and shoulders hurt, but my legs felt like I had never worked out before! It was brutal!! I work long hours and tire easily. I'm sure that doesn't help either. So I've been on a mission trying to find things that work for me. Yesterday I purchased a weighted (2kg) hula hoop. Love the hula hoop!! I was playing around with it while watching tv lastnight. I have also been swimming in my pool as much as I can, last week I swam 4x. I have found if I use a pool noodle to support my upper body (its natural instinct for me to use my arms when in the water, the noodle keeps me from doing that) and I do some lower body work in the water. I walk of course too, but sadly even that can make my shoulders sore afterwards from the swinging of my arms. I'm struggling with a few issues really. One being that I don't have the energy I had prior to the accident. Most days its enough just to get my physio "homework' in after a long work day. And another issue I struggle with is how far to push myself. Seems like a fine line between pushing myself to do better/more and going too far and causing a setback with my healing. I know that there is soreness after a good workout, but when I'm sore all the time I have a difficult time pushing myself to that point when exercising now. I hope that makes sense. The best way to describe my soreness is like a constant strain that goes across my upper back/shoulders, and stiffness in my neck. I'm wondering if anyone out there has suffered an injury similar to mine and can share what exercises they did to keep in shape while recovering. I'm desperate to be a bit more active!! I have slowly been putting on weight and have been losing tone and definition.