I don't recall to be honest, and I don't have the old manifold now to compare. But it makes sense that the tubes in the manifold are just bent tube, welded to a plate. I can't imagine there are different diameter tubes on either side. I just checked mine, all the small lines are 3/8" ID on my truck.
Just a note: The "manifold" the soft lines get connected to - there are two different sizes. For the small diameter hoses, my FJ60 had 1/4"ID hoses, though my '87 HJ60 had 5/16"or 3/8" hoses. Either way, they're not all the same. I realized this when I sized my new hoses with the one out of...