David - by the sound of it, you have torn a hamstring. I have just recovered from exactly that, and I was undergoing rehab with a physio and was "banned" from running for a full 4 wks.

Only this week was I able to get my trainers on for the first time since July.

I too, carried on after a brief  2 week rest and then damaged it again in pulling the starter motor on my lawnmower would you believe! In other words, I came back to soon and in total have missed 6 wks running!

My advice - see a physio and they will treat it and, give you a strengthening programme to work on, so you should come out of it stronger.

David, the toe problem, Google 'Mortons Neuroma' and see if that rings any bells with you. If so then the first thing to do is to make sure that your shoes aren't too tight around the balls of your feet.

Definitely see a sports physio (make sure it's a sport physio and not a general one)/. They will see if you have any tightness in your hamstrings/quads/itb, give you some stretches to do before and after your runs along with some exercises to strengthen your muscles to support the hamstrings. 

I also highly recommend regular sports massages to keep things nice and loose. Have a look on Youtube at 'foam roller hamstring exercises' too.