In reply to Dave Heaton:
Your goals are quite diverse, from a physiological point of view: weight loss, strength gain and stamina / cardio improvement. You may find you get the best results by focusing mostly on one specific aspect for a given period, then switching emphasis. That doesn't mean entirely neglecting the other aspect: your schedule of 4 days training/week works in perfectly at a 3:1 training ratio.
For real-world strength training, it's worth reading this book:
http://www.amazon.co.uk/Starting-Strength-Basic-Barbell-Training/dp/0982522...
As this regime is concerned only with the development of genuine and absolute strength, it uses only the barbell. As many aspects of barbell movement are highly skilled and not intuitive, it's worth reading up on the techniques you'll use to ensure both efficacy and safety (or even better, you could seek instruction from a reputable powerlifting coach). 12 weeks or so on this or a similar 5x5 regime will be tiring, but will certainly translate to improved strength and power for bouldering, with the bonus of a massively improved core.
For CV, I'd highly recommend the indoor rower. Like you, I've had to stop running thanks to ongoing knee pain: I've used the rower as my sole 'cardio' for 4 years now, hugely improving endurance and remaining injury-free. Again, worth taking the time on learning safe technique:
http://www.concept2.com/indoor-rowers/training/technique-videos
As for weight loss, you probably know that this is largely mediated via diet as opposed to activity; as such it's simply a case of lowering calorie intake over time. However, during any period where you're working to build strength, you will find the process easier with higher-than-normal levels of protein in your diet, and with running a slight calorie surplus. It's easier to remove pudge after such a phase than it is to gain strength while being calorie-restricted (although it's not impossible if you're really determined). As such you'll find weight loss easier if you choose to pursue it during a CV development phase.