the stock DOHC ZC exhaust manifold will not match your DX exhaust - the DOHC ZC used a 4-2-1 design, so the manifold has 2 outlets where the downpipe connects - you can use DX or Si header and it will match up or you can swap the downpipe for one from 92-95 Civic EX - you may have to modify it slightly to match the exhaust, but it will bolt to the ZC exhaust manifold
we have swapped over 2 dozen ZCs into all models of 88-91 CRXs and Civics and the only problem we have had with the hood hitting the timing belt cover is on ones that have the sound deadening insulation thing on the bottom of the hood - we just cut out a small area of the insulation right at the timing cover and then no problem