Hi, I'm also a graduate student and I pretty understand your feeling. I think you are confused with the relationship between small signal model and real circuit. If you really know how to use small signal model to calculate gain without CLM and body effect, there should be no problem when they are added in. All you need to do is add those parameters (gmb, ro) into your small signal model and calculate as the same way. I understand it may become very complicated especially you have several transistors and you have to consider CLM and body effect for all of them, actually it only takes you time when solving equations. Try practice more and you will get there eventually.
For books, I really do not think you need a book to learn these basics. But if you need more practice, I would recommend Razavi's Design of Analog CMOS Integrated Circuits.