thermoquad manifold, do i need these ?

Leave them alone. The only thing you need plugged is the outside flange where the EGR bolts on. Trying to plug two holes in the bottom of the intake that you can hardly get to is stupid. Plug it where it's easily accessible. On the outside of the intake at the EGR flange. Just make a plate the same shape as the flange, drill the bolt holes in it, use a gasket or high temp RTV and bolt the plate on. Done.

I don't know why in the hell so many people turn things into such a complicated task when the easy approach always works. It's your intake. Do it like you want.