The dirty little secret is that noone actually knows how the body works. There are very few peer reviewed articles on "gaining muscle".

The only real facts are:

• To gain weight, eat more than you need to.
• To lose weight, eat less than you need to.

To gain muscle you will gain fat as well, that's how it works. Exercise, lift heavy things, run (edit: climb trees). Try to imagine being a hunter/gatherer - that's what we are after all.

Good luck.