The man in the pipe had the number 2 as a tattoo, not the number 1. This kind of makes it difficult for it to be Zack, considering Zack didn't have a tattoo.

He's gone because he left to attempt to reach the Reunion. The man next to the pipe implies this.

It was Cloud who suffered an adverse reaction to the Jenova cells, not Zack. If Cloud had recovered from the delirium, there's no way Zack would still be suffering from it, considering it never affected him in the first place.

There is no plausible theory that links the man in the pipe to Zack. Zack is dead.