Question

1. I would not do so, it I were you.
2. I would not do so if I were you.
(Are both okay? Do we have to delete the 'comma' in #1?

3. He could come earlier.
4. He could come earlier if he were not busy.
(Does #3 mean #4?)

4. He could have come earlier.
5. He could have come earlier if he had made haste.
6. He could have come earlier if he had not been busy.
(Does #4 mean #5 or #6?)

Answer 1

In #1, I take it you mean "if" instead of "it" - right? The the comma is not needed.

All the others are correct and are similar in meanings, but not identical. The "if" clauses give reasons, but not all reasons should be assumed to complete the meanings of sentences 3 and 4 (the second 4!).