Welcome aboard CF, Jefmo39.
What model Yanmar
or if not know, how many cylinders and approximate age?
All the Yanmar injectors I'm familiar with just pull out once the "top" retaining collar is removed. I say "just pull out" but sometimes it can be a bit difficult.
I'm confused though with your description of "pretty much flush with the head". IME, they are not flush at all unless you have already disassembled the injector body.