No. The CRV manifold is meant for DOHC b-series motors. Even if you had a B16 engine in your Civic, the CRV's B20 intake manifold wouldn't clear, it's just too high. I'll take a picture of my down CRV's intake manifold now, it's ridiculously high.
SOHC D engines have many interchangeable parts; hence why you can use a y8 mani on a y7; or y8 head on a y7 block.
DOHC B engines have many interchangeable parts, hence why people make LS-vtec or CRVtec motor builds (mating a non-vtec or high-compression block with a vtec head)
I don't know if this picture does it justice but:
Anyways, for 97-01 CRV parts into a 96-00 Civic, I took the CRV's cluster, aircon pulley & belt, miscellaneous clips and screws, an aftermarket player + the din casing frame (whatever it's called), the sun-visor clip and a couple of other parts and used them into my 99 Sedan... hoping to get the engine too.