Those sentences are wrong: they do not follow the grammatical rules of English, and natives would not say or write them. When a verb has multiple auxiliaries, in a question, the subject comes immediately after the first auxiliary and before the second auxiliary. The same thing goes for adverbs that are placed before the verb, such as ever here; it would also apply to a negation.
Might you ever have read that book?
Might you not have read that book?
These sentences are grammatically correct, but they sound weird. “Might” is uncommon in yes-no questions since it refers to a possibility; an answer “yes, I might” doesn't actually say anything. “Might” can be used in a question, but it has a de-intensification effect, whereas “ever” has an intensitification effect.
Might you have read that book? Perhaps you read it a long time ago in school and you've now forgotten it?
Have you ever read that book? If you did, I'm sure you'll remember it.
As for “*Might you had …”, it's ungrammatical for another reason: “had” is a past tense (it could be either a simple past or a past participle), but “might” must be followed by an infinitive. To combine “might” with a past tense, you need to use a compound past (“might have read”), and you can't make a past perfect (if a past perfect is needed due to tense sequencing, a compound past will be used instead).