Runners returning to race training after illness

I was diagnosed with pneumonia on March 13, finished my antibiotics on March 17 and slowly did my first treadmill run on March 22. I've only managed 2 other low distance runs since then, partially because of lung function but also because of time. I was given the okay by my dr to get back to my half marathon training as long as I'm keeping an eye on my peak flow, taking my asthma meds and sitting out a run if I feel too bad. Anyway on the three runs I've done, the first after 2 weeks off because of the original chest cold, I've had pain after they were over, muscle soreness, hip and quad pain and general tiredness. Both pairs of my shoes are broken in but not worn out, so it's not that. I assume it's related to recovery but don't know if I'm just being impatient. Have any runners out there had to deal with something similar? How long did it take to get back to normal training after being ill? I've got a half marathon coming up on May 5 and at this point I don't know if I'll be able to do it.