I was in loads of pain for a long time when I first started riding too (mostly my neck and butt). Nowadays my quads are still almost always sore but the rest of the stuff has gone away. It took almost a year for me to truly build up "cycling muscles". I also had to get my fit right and find a saddle that works for me. I say give it more time. Increase your mileage gradually and give youself sufficient recovery time. Stretching, core exercises, and massage really help too.