If you can, try working with a personal trainer. It doesn't have to be a long term thing -- maybe once a week for 4 weeks? The benefits of a personal trainer is that he or she will understand what your goals are and help you design a workout plan that will work for you. After you stop working with the trainer, you will still have these workouts/exercises. I recently worked with a trainer for about 9 weeks. While I have yet to actually go back to the written workout plans he designed for me (I will, someday soon), I've been able to take these exercises and incorporate them into my own plan. Prior to the training, I usually just got on the elliptical for 20-30 minutes and that was that. Occasionally I used some of the machines at the gym. Through time with my trainer, he explained that I was better off mixing cardio and weights to my routine (even if I only had 20-30 minutes to spend at the gym) than to spend 20-30 minutes just doing cardio. Moreover, I learned about interval training and realized that doing 10 minutes of cardio with intervals (ie: hard for 30 seconds, easy for 1 minute) was better for me and produced better results than going at an even pace for 20 minutes. I also learned that I should mix up what kind of cardio I did (I hated the bike, but now I try and use the bike a couple times a week). Now, I usually warm up with 10 minutes of cardio intervals then spend 30 minutes on the machines/light weights/pushups/situps before cooling down on with intervals on the bike for 10 minutes or get on the treadmill.
It might be helpful to introduce jogging to your routine. Cool Running's Couch-to-5k Running Plan is really helpful. They want you to go slowly and recommend repeating weeks as many times as necessary until you feel comfortable to move on. I followed this plan a couple years ago and then life got in the way with grad school, but I just added it back into my exercise routine. It's doable too. The first week consists of alternating 60 seconds of jogging with 90 seconds walking. Intervals.
Anyway, good luck!