With both the perfect and the progressive, try thinking in terms of a point in time. When you use the present perfect, it is understood that you are referring to the current point in time (the present), but with the past perfect you need to specify that point otherwise it doesn't make much sense.
Your sentence 'he had read the book' isn't much use on its own, but if you specify the timing, you can see the benefit of using the perfect: 'I lent him the book when I left for work, and when I got home he had already read it!'. It's similar in Japanese: 日本に戻ったら桜がもう落ちていた when I returned to Japan, the Cherry Blossom had already fallen.
I don't really know how to answer your last question in terms of Japanese, but in English it is acceptable to say both 'he has seen it already' and 'he saw it already' in such a situation. I'd say they're basically the same, but the first one has a nuance of 'so he won't want to watch it again', whereas the second just simply states the fact.
Also, like the other guy said you don't want to think in concrete English terms, I was just trying to give you a different perspective because it helped me understand it before. Try to stick closer to my second explanation (it's a mixture of stuff I learnt from two good textbooks), or better yet get a decent grammar dictionary or textbook yourself, since there's all sorts of other stuff you'll need to learn anyway. I'd also recommend reading some simple books or manga regularly; the more you see this stuff in action the quicker using/recognising it becomes second nature.