1962 Exhaust manifold nipples?
 

On the passenger side exhaust manifold on my 62 GP right above the exhaust pipe flange connection there are 2 nipples sticking out. What did these used to be for?

I’m guessing what I’m seeing are the remains of an exhaust manifold heat riser valve?

That is very likely. If the flap and shaft are gone and you don't mind doing without, the shaft holes can be brazed up pretty easily