It's my job to be in shape so don't hate on yourself too much. You'll get there. A good program that I use is do 3 types of runs a week. I do it Tuesday, Thursday, and Saturday for a month then switch to other stuff for a month. I run an 2.5 mile interval run on Tuesday. That's usually a 200-300m sprint followed by a 100-150m jog. A 5K on Thursday. Then, 4-5 miles on Saturday. On the Saturday run I go as fast as I would for a 5K for the first 3 miles and then slow down for the last 1 or 2 miles. That program got me an 18:25 on my last physical fitness test which is a 3 mile run.
Just by looking at your post, it looks like you're going for a triathlon type workout. There's something called a "sprint triathlon". I believe its swim 500m, bike a 10K, run a 5K. Those are a blast and only take about 45 minutes to 1 hour. Fun way to get into it without frustrating yourself.
Above all of this though Crossfit. If you've never done it, I can give you instructions on how to use the website. After that, you can self train. That's what's great about it. I've never been formally trained in Crossfit but can post comparable times to what you see on the website. Reverend Hellhound is better at it than me though. He can help you out too. He's always on this thread.