Exhaust studs with headers?

Your correct in that the studs are I. Water jackets. The header can be slid into ace with them in the head. While installing the header, the engine need to be released from the mounts in order to tilt and raise it up for clearance.
Also disconnect the battery wires and other ground cables and wires from the engine. You will need as much clearance as possible.

When I do headers, I use the studs to hang the header for a rest or to reposition myself above or below. Headers are not easy to install. Have a buddy at the ready.