You're not looking at it the right way. A 95 Si uses a D16Z6 engine. An Si-R II (which is a stupid way to term is, btw), a.k.a. B16A2 is a completely different engine. They have different heads completely and the block height is differernt.

You have to get a header for the '99-'00 Si because that's what header fits the B16A engine.