The correct answer is D. I was struck on the head by a stone.
The other options are incorrect because they do not correctly place the emphasis on the fact that the stone struck me on the head. In option A, the emphasis is on the fact that I was struck, but it is not clear what struck me. In option B, the emphasis is on the fact that my head was struck, but it is not clear what struck my head. In option C, the emphasis is on the fact that I had been struck, but it is not clear when or by what I had been struck.
In option D, the emphasis is on the fact that the stone struck me on the head. This is the most important information in the sentence, and it is the information that is most likely to be remembered by the reader.