It's all in the cams, everything else is pretty much the same.
The '85-'87 ZC motors have a dual plate throttle body just like an '85-'87 SI but the design of the intake manifold is essentially the same as a D16A1 (ZC also has an EGR on the IM).
The '88-'89 Integra ZC IM is almost exactly the same as an '88-'89 D16A1, and the '88-'91 Civic ZC has the largest IM (which is what I'm using).
The '88-'89 Integra D16A1 and '88-'91 Civic ZC motors have lighter rods and a higher compression ratio than the '85-'87 D16A1/ZC1 motors.
Here's a pic of an '88-'91 Civic ZC intake manifold on my '89 D16A1 with ZC cams (amongst many other mods).
More info here:
http://www.cardomain.com/ride/2278318/1