Still a bit flat :(

Had a decent run this morning, 7k exactly in 40:33.
Have to say that although the time was fine, it took me over a kilometre to be able to run and feel comfortable without pain/discomfort in my feet. Once I had that first k or so under my belt, I started to feel a bit more steady & fluid, but still flat on the energy levels. Whilst I wasn't exactly struggling, I felt like I was working harder than I was a three months ago on a day doing the same run/distance? Not sure if the body is still recovering from the flu last week, or whether it's still a bit of a hangover from the HM.
Since running the HM, I have not felt 'fresh' in any run since. Wondering whether I did a bit of damage/used up the mitochondria in the muscles, when running the last few k of the half in what I suspect was an anaerobic state. If that is correct, how long to recover fully I wonder?
I was hoping to be feeling really fresh again by C2B and therefore be able to attack a really good time (for me), but am now a bit concerned. Perhaps I am over analysing this and it will all come good but wouldn't mind any feedback anyone had to share about their experience after a big/tough run.