I came across your and Mr X's publication
I came across you and Mr X's publication
CMOS 16th edition says in 7.22 that it depends on whether you mean the nouns as a single unit or as discrete units; that is, whether the object possessed is the same or different for those two nouns. Since you're talking about two authors responsible for a single publication, not two authors of multiple publications, the nouns are a single unit. "I came across you and Mr. X's publication" is correct.
But there's no question that it is awkward because it's in the second person. (Compare to this third-person sentence: "I came across Dan and Steve's publication.") Reworking the sentence is definitely the way to go.
"You" sounds wrong and "your" awkward. Turn it around: I came across "Charlie Manson reconsidered" by you and Mr. X.