In the entire bookstore, this was the best book which I liked
Or
In the entire bookstore, this was the best book which I have liked
Or
In the entire bookstore, this was the best book which I had liked
None of those are right. You can say this: In the entire bookstore, this was the book (that/which) I liked best.
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None of those are right. You can say this:
In the entire bookstore, this was the book (that/which) I liked best.
You're organizing your sentence incorrectly. This is more natural in English:
Of all the books in the entire bookstore, I liked this one the [best / most].
(Not 'have liked' nor 'had liked'.)
CJ