You need a structured program. I don't think you'll get there without some outside influence.
Agreed. I was in need of getting back into shape after surgery, and it really helped me to sit down one night and focus only on getting a program planned to the T. Others might not need that much structure, but I do, and am just using an example.
http://www.stewsmith.com/linkpages/toughworkouts.htm
The above link will take you to a core/upper body calisthenic program which I have been using a modifying for the past three weeks. The benefits have been incredible. I do the core 7x a week, and mix upper and lower body on alternating days.
Also, with advice from his webpage, various internet pages, and a mustang from my unit, I've been doing a lot of interval running, which I have also noticed phenomenal gains. (Do a search on here for VO2 max, that thread has some good info, and researching the internet will help you out too, they all tie in to interval running)
The bottom line though is in your position 3x a week isn't going to cut it. Every other day should be a big cardio workout day. Once you drop lbs EVERYTHING will be easier.
Push yourself each week, but not unrealistically. Taking at least 3:00 off a run time and doubling everything else won't be easy. However, once you find a good momentum you'll start noticing bigger and bigger gains.
I would recommend you find a good starting point where you're getting a tough workout, but not physically dying, then set a goal to do 10% more or faster each week.