I know this is an old thread, but I'm having the same problem and the "transform" isn't fixing it.
I bring the two files, one duct one condenser piping, into Revit. I dimension the x and y difference between the two. I append the condenser piping model to the ductwork, then right click on it in the selection tree and type in those same dimensions in the x and y, but negative. Is this the right procedure? It's not giving me the right alignment.