"I was gone" vs "I had gone"

What is the difference between the following two statements.

By the time you sent me the email, I was gone.

By the time you sent me the email, I had gone.

Both of them clearly expresses what had already happened.

If there’s a difference between the sentences in your edited question, I would say that ‘I was gone’ emphasises the state of having gone and that ‘I had gone' emphasises the act of going.

Your sentences in fact contain two different verbs: to go and to be gone. The verb to go can be postmodified as in go home, go shopping, go to the beach, etc. But the verb to be gone (which has the meaning of disappear or not be there any more) cannot. So he was gone home is ungrammatical.

The first sentence:

By the time you sent me the email, I was gone home.

is grammatically incorrect. In English, you can say either "I was gone" or "I was home" but not "I was gone home". This is because the verb was followed by either home or gone represents the place where the speaker is. That is, the speaker was somewhere. To say was gone home incorrectly uses was.

The second sentence is in correct simple past perfect form, and is grammatical.