As beneficial as HOT-ROX is for fat loss, it's simply unnecessary in this guy's current situation. A morbidly obese beginner who's still getting his exercise program in place (um, no offense poisonblood) has no reason at all to be considering fat burners.
Sorry to hear about your loss, but good for you for getting back to taking care of yourself.
If what you've been doing has been working, there's something to be said for sticking with the plan as is, or at least making minimal additions (like adding strength training. That's definitely a must-do.)
I'll bet that as we drop some fat, your back and ankles will eventually start feeling better, since they're not supporting as much weight.
Gotcha, and if that's been working, awesome, stick with it. But just to be a nit-picker, if I'm reading it right, your "no carb day" is really a low carb day and your "low carb day" is really a moderate carb day.
This should definitely help your knees, back, and ankles.
If you can get three good cardio workouts and three good weight workouts every week, that'll be fine. Whether you do cardio and weights on the same day or alternate one day just weights with one day just cardio is really up to you. If you can fit in more days, that's fine, but I'd still keep one or two days of no training at all, to prevent getting burned out.
5/3/1 is a lifting template designed by Jim Wendler. There's an article explaining the basics here:
Glad to see that you're doing some weights, but you'll get even better results if you focus on "bigger" and more challenging exercises that work multiple muscles at the same time.
For example, some kind of bench press (dumbbells, barbell, or machine) would be a better choice than the machine fly, because the press will work your chest, some shoulders, and some triceps, while the fly only works the chest.
Bigger movements like that, called compound exercises, are a more efficient way of building strength and muscle, and boosting your metabolism with each workout. You can still do some arm exercises (curls, extensions, etc.), but I'd try to do some kind of squat or lunge, a pulldown or a row, and some kind of chest press in each session also.
Also, instead of lighter weights for high reps, try to use a weight you can only lift for no more than 8-12 reps. Light weight, high rep work won't build much strength or muscle.
It might all seem like a lot of work, but remember that it's worth it and it'll get you where you want to go... less fat, more muscle, and in better shape.