the sensor on the end of the exhaust camshaft is the cylinder sensor - the D16A6 engine originally in your Si had the cylinder sensor inside the distributor
the original Si distributor has a round 7-wire connector that plugs into it - the wire colors are: WHITE that goes to the Igniter - another WHITE and an ORANGE that go to the Crank sensor - ORANGE with BLUE stripe and WHITE with BLUE stripe that go to the Top Dead Center sensor - BLUE with GREEN stripe and BLUE with YELLOW stripe that go to the Cylinder sensor
the DOHC ZC has a rectangular 5-wire connector - the wire colors are: WHITE that goes to the Igniter - another WHITE and an ORANGE that go to the Crank sensor - ORANGE with BLUE stripe and WHITE with BLUE stripe that go to the Top Dead Center sensor
you will notice that (5) of the wire colors and functions are the same for both, with the difference being that on the DOHC ZC, the BLUE with GREEN stripe and BLUE with YELLOW stripe wires for the Cylinder sensor need to run to the sensor on the exhaust camshaft which has matching wire colors
the best way to connect it is to obtain a rectangular 5-wire distributor connector, with wires, from any 88-91 CRX/Civic STD, DX or LX with the DPFI engine (which will plug right into the DOHC ZC distributor) and mate it to the wires in the Si engine harness, matching color for color of the wires and extend the BLUE/GREEN and BLUE/YELLOW wires and connect them to the Cylinder sensor, matching color for color
you will notice that you have 2 white wires - you need to make sure that you connect the right white wire in the harness to the matching white wire in the distributor connector - attached are diagrams of the wire locations in both connectors
FYI - the BLUE/GREEN wire runs to ECU pin C1 and the BLUE/YELLOW wire rund to ECU pin C2
the factory ECU for the DOHC ZC is the PM7, however, it will run about the same with a PG7 from 88-89 (not 86-87) Integra - you can also use a PM6 from the Si - it will run about the same with the PM6, however, the PM6 has fuel cut-off (rev limiter) about 500 rpm lower than the PM7 or PG7 - the extra 500 rpm does make a difference