All D-series intake manifolds will bolt on. the short answer is yes. You don't swap fuel injectors/rails, they will bolt in fine.
Note that 99-00 Civic EXs have air injection so if you use a Z6 manifold, you'll have to do some hole plugging.

The D16y8 engine with the AUTO transmission equipped engine works like the y7....it has the IACV in the throttle body. The y8 with the MANUAL had an IM with two holes and the IACV on the back of the plenum like the Z6. So if you use the z6 manifold on an automatic y8, bring your IACV with you....or plug the two holes and use the d16y7/d16y8auto throttle body with its IACV. One is a 2 wire and one is a 3 wire, there is a trick to do if you change it, but its not too hard.