Sounds like a dilema! I don't have an answer, but a question.... When the enigne was rebuilt, was the crank checked for alignment? Thats really SOP and if it was, you should be able to put that out of your mind--just one less thing to worry about.
BTW, a friend w/ an '85 300D has had transmission noises for the last 2, or 300,000 miles. He is appraoching 500,000. Sometimes these cars refuse to quit--but you never know.