Plug the conversion harness C101 (large flat grey) connector into your 02-04 style engine harness near the ECU plugs. 

Plug the conversion harness 'E' (white) connector into your KPro ECU.

Secure the relay out of the way near the ECU.

Route the oxygen/air-fuel sensor connector through the firewall to your air-fuel sensor on your exhaust manifold or header.  Extra length is provided on the 4-pin oxygen/air-fuel sensor connector harness so that you can route this in any way desired through the firewall.

Plug the 22-pin green connector into the green 22-pin connector on your dash harness.  This is the connector that originally plugged into your Civic's engine harness.

Route the remaining long portion of the harness under your dash to the driver's side.  You can either route it through the firewall on the drivers's side to your driver's side shock tower, or, pull your chassis harness on the shock tower back into the cabin and connect it there. 

The loose yellow/green wire at this connector should be routed to your K series engine's 1-pin temperature switch.  This is used for the temperature gauge on your dash.