Factory pipe makes their manifolds fit 62Ts by drilling the bolt holes larger. Then they find someone who is incopetent and probably hates his job to take a hand held cutter and raise the top edge a little. Seriously, DO NOT let Factory Pipe modify a manifold for you.The 62t port is the same except it's about 2-3mm taller on the top side. You can "port" the 61x manifold up a little bit to match the 62t port fairly easily. I'm guessing that's exactly what factory pipe did for their 62t manifolds but I have never actually seen one so I don't know.
Most of my junk is built from sketchy used parts but from what I've seen most manifolds don't fit either port all that great without some touching up.