Beginner runner and knee pain?

First of all I want to start out by saying that yes I am overweight by about 65 pounds. I'm a female 26. So I made the decision 3 1/2 weeks ago to get healthier for not only myself but for my children as well. I changed my diet and began exercising. When I was younger I was very physically fit. Ran 4 miles daily and biked 4 miles daily. I also played soccer for my high school. I was so active that I got Osgoodshaluters disease, common in teen athletes. Well when I began going to the gym a few weeks ago I began with the tredmill and bike. I would warm up for 5 minutes and then jog for 1 minute and walk for 2 and I would alternate the two for 20 minutes then 5 minute cool down. Then I would get on the bike machine for 15 minutes, also with a 5 minute cool down. I didn't want to overdue it right at the beginning. Well I very quickly built up a stanima and increased my running daily to 2,4,6,8,10 ect minutes at a time...Now in 3 weeks I can run for about 18 minutes non-stop at about 7.8 MPH....Well Monday I guess I pushed myself a little to far and I ran for an hour at 8.5 with only one walking break of 4 minutes. My knee wasn't hurting at all while I was in the gym and I felt GREAT when I left...It was the next day I woke up and couldn't really walk, straighten my leg fully and bare weight. I have perscription IBprofin 800mg and I've been taking them to help with the pain and the swelling. I have been going to the gym everyday but I did take yesterday off. Today I did go and my knee was hurting, but I pushed through the pain and the pain eventually stopped but came quickly back about an hour after going to the gym. The pain is on the inside/left side of my right knee. Not sure but I think that's the MCL?? My question is should I push through the pain and continue, or how long should I stay off it?? Also what do you think the problem is? Overuse, or maybe a serious injury? I know you're not DR's but maybe some of you have had a similar experience....Any suggestions would be great!!! Thanks in advance