"Was reading" refers to the time during which you were actually doing the reading. "Had read" actually refers to the time after you had stopped reading. "Read" (simple past, since the simple present is spelled the same) simply mentions that it is something you did and makes no reference to whether we are talking about before you did it, while you did it, or after you did it.
Was reading is English past progressive tense, which refers to an ongoing action in the past. (If I was reading the book at eight o'clock, then the time under consideration is eight o'clock and that's when the reading was happening.) Had read is English past perfect tense, which refers to an action that occurred before the time in the past that is under consideration. (If I had read the book yesterday, then the time under consideration is probably today, but the reading happened before that. Read is English simple past tense, and it's the tense English uses to indicate perfective aspect in the past, though it's also the tense English uses to indicate other aspects like habitual. (If I read the book yesterday, the time considered is yesterday, which is also when I read the book. I might have simply performed the action of reading until I stopped [perfective aspect], or I might have read on and off during the day [habitual aspect].)
Klingon -taH continuous and -lI' in progress aspects are close to English progressive tenses. Klingon -pu' perfective and -ta' accomplished aspects are close to English perfective aspects expressed with simple past tense. English perfect tenses (have read, had read, will have read) are less similar to Klingon perfective suffixes, but they are often used to mean something very similar. The meanings between English tenses and Klingon aspects overlap, but differ quite a lot in expression.
why isn't "I am reading that book yesterday" work, isn't the tense not a thing
In English things we did yesterday are stated in the past tense: "I am reading this book today. I was reading that book yesterday." Depending on how you define the word "tense" it might be helpful to think of it as if "tense" exists in both English and Klingon. In English we change the verb to represent the tense even if a time stamp is present. In Klingon the verb does not change to match the tense, but time-stamps or other context usually makes the tense clear.