I really want to run but I don't want injuries, any advice?

I used to run quite a bit (not in any real competitive way but) but I stopped about a year ago. I started it back up by running 3K every morning for the past week (run 5, rest 2, run 10, rest 2 etc.) and it's been pretty killer on my muscles. I stretch before and after for at least 10 minutes, I do a warm up and I eat the appropriate post-run and pre-run foods but they're still pretty achy. I notice that even if my muscles are sore in the morning but I push through my 3K anyway that they don't hurt as much after about 5 minutes and they only start to get sore an hour or so later. Anyways it's about 8:30pm over here and I really wanna go for a 30-40 minute run but I'm wondering if that might be over doing it seeing as my muscles are still adjusting and recovering?