In Australia the LD340 is a really, really rare piece of merchandise, and this weekend gone I found mine needed machining after Zero deck and thinner head gaskets.
I agonised about cutting it, but I bought the thing because I wanted it for this engine, so it gets the chop.
Cut the intake surfaces of the heads, not the manifold. Then you'll be able to switch manifolds if the mood ever strikes you, and you won't have to have the new manifold cut (again...).