Well, you have presented two questions here that need to be addressed separately, I think.
First, the verb tenses are all grammatically correct. So, unless you provide context, we have no way of knowing which is the most suitable for the meaning you wish to express. For example, 2 and 4 can be easily clarified with an adverb of time or additional information.
2) She has always blamed us for the dispute, especially you and me.
4) She had blamed us for the dispute, especially you and I, but she's changed her mind now that she's spoken to Robert.
As for whether it should be "you and me" or "you and I," strictly speaking I think "you and me" is correct, since this is an indirect object of the verb to blame. But there are plenty of people who would say "you and I" in conversation.