I just finished WD3 today, too, so I totally get how tough it is.... but then it's so damn exciting when you finish that 20 minutes!! At this point I'm on pace to complete a 5K in about 45 minutes (I'm signed up for one in about a month). But I have found running two days in a row does not work well at all for me. I've been putting one or two days in between and it feels much better. My legs and back have felt okay - I was worried most about my back - but, strangely, it's been my right arm and shoulder that have been very sore, so I'm trying to be conscious of trying not to tense up.
Good Luck!!