Are the following sentences natural to a native ear?
1. I have had John work on two of the seven files. ( I want to convey that John is still working on the two files, but I am not sure that this sentence conveys that meaning)
The sentence is fine, but it does not convey the meaning you want. It's entirely possible that John has finished working on the files.
2. It would be good to have him sit with you while you do it, so that he can also learn it.
No comma required between "you" and "while". I would probably say "he can also learn how to do it" at the end.
3. These all factors called out to me that you are the culprit.
All of these factors suggested to me that you are the culprit. (This is OK although I would probably use either "suggested/you were" or "suggest/you are".
Student or Learner