I've heard of this. The crux of it is the basic supposition that the human body was created "broken" and that without and without constant attention to just the right combination of foods, overindulgence, poor nutrient assimilation, gas, blood disease, liver problems, kidney problems, bacterial toxins in the gut (the list goes on and on) will occur.
So, as you mentioned, different types of foods need different enzymes to digest them. But it is believed that if you combine too many different foods at once, the body will become "confused" and will be unable to make all the necessary enzymes at one time. Then, bacterial fermentation will result and blah, blah, blah.
Okay, well, I actually do think there is a kernel of truth in it. The amount of food you eat, and the combination you eat them in, does affect digestion. The problem is that some of this "new age" dietary advice takes a simple idea and expands on it past the point of all reason.
For one, a healthy body is very efficient at digesting a great variety of foods. For another, it gives one small aspect of healthy nutrition a life all it's own, and ignores scads of other criteria such as some of the things Sleazy mentioned, like insulin response, which is not just important to bodybuilders.
The main thing, though, is that it's not based on any real science, but on mistaken assumptions. You take someone who has been leading an unhealthy lifesyle for long enough - overeating, eating overprocessed foods, gorging on snack crap, drinking heavily, basing most of their diet on one thing, like eating most all meat, whatever, and you switch them to a diet of healthier foods in general, at a proper intake, and after a while they're going to feel better, no matter how you combine the food. And it could be any number of things that is causing that, and probably is.
Of course I don't know all the ins and outs of what was reccommended to you, but some of these diets are so complicated and unmanageable - I mean, you're going to be all the time worrying about every little scrap of food you put in your mouth, if it's the proper timing, the proper combination, you are lible to get sick just from the stress.
The idea that the body can't produce the enzymes it needs, well, that, in a nutshell, is just hogwash. But that doesn't mean that everything they say is untrue. I certainly agree with the idea that all the food you eat should be as nutrient dense as possible.
I don't think any of it is very compatible with bodybuilding. I agree with the basic dietary guidelines that Sleazy has given you. You definitely need more protein. Think about lean protein sources, complex carbs like whole grains, green vegetables, healthy fats (especially your EFA's).
People here can give you more specific advice once they no your specific goals.