99-00 Civic:

Engine info for 96-98 civic can be applied.

Wiring: Part 1

Wiring info is simliar to that of 96-98 civic but slightly different.

If you have a non-vtec civic you will have to perform these mods to your EWH in order to be compatible with an OBD1 VTEC engine: (1) add the respective wiring for VTEC (2) wire in the KS (unless you plan to use a P28 ecu) (3) *perform the IACV mod (4) change your dizzy plug to that of a 99-00 Si, 96-98 civic, or 96-01 integra large sized dizzy plug.

*The IACV mod consists of converting a 3-wire IACV plug to a 2-wire IACV plug, as explained in my diagrams below. All OBD1 engines use a 2-wire IACV:
http://www.ff-squad.com/tech/w...0.jpg
http://www.ff-squad.com/tech/w...g.jpg

For whatever reasons, Honda switched to a smaller style dizzy plug on all 99-00 SOHC civic's. This plug has to be changed if you plan to reuse your SOHC EWH on the OBD1 engine. You'll need a 99-00 Si dizzy plug or a 96-98 dizzy plug that you'll need to depin and mate to your 99-00 CX/DX EWH.

As an optional choice its highly suggested to fully switch over to a 99-00 Si EWH which in contrast is simliar to using an EX harness in a 96-98 civic. But again, the 2nd 02 sensor is part of the Si's cabin harness. So you will have to manually wire in the 2nd 02 if you ultimately plan to use a US OBD2 ecu.

Wiring: Part 2

Wiring info from 96-98 civic can be applied.

ECU

You have 3 options in this department.
Starting from easiest to hardest..

(option 1)
Use a 99-00 Si ecu

PROS: This is the easiest solution as this ecu plugs directly into your 99-00 EK, but you will need to perform the CKF bypass trick. Will be able to pass smog depending on certain variables. 99-00 Si ecu is compatible with US OBD2 scanner tools.

CONS: CFK bypass trick is required; OBD2 ecu reprogramming is very scarce; 2nd 02 sensor required.

ROS: This by far is the easiest solution as this ecu plugs directly into your EK and doesn't look for a VTPS

CONS: OBD2b>OBD2a jumper harness is required ecu upgrades are scarce; will not pass smog with a JDM OBD2 ecu as they do not communicate with US OBD2 scanner tools; 115-120mph speed limiter.

(option 2)
Convert to OBD1 ECU via OBD2b>OBD1 jumper harness and simply use an OBD1 ecu (JDM or US) to power the engine, such as a reprogrammed P28.

PROS: OBD1 ecu's rule in general as they are easily reprogrammable and do not look for additional sensors (2nd 02 & CKF for instance). OBD1 ecu's are very forgiving and not as sensitive as US OBD2 ecu's are.

CONS: cannot pass smog, VTPS required to be wired in.

(option 3a)
Stay US OBD2b spec by using a 99-00 Si ecu; 00-01 Integra GSR or ITR ECU (requires Immobilizer removal!)

(option 3b)
Convert to OBD2b spec via OBD2a>OBD2b jumper harness and use a 99-00 Civic Si ECU.

PROS: Can pass smog if CKF bypass trick is successfully performed in an integra or Civic Si chassis. If your Civic cx/dx is B-series BAR'd you should be able to pass smog too.

CONS: 2nd 02 needs to be wired in and working.

(option 4)
Run a JDM OBD2 ecu via OBD2b>OBD2a jumper harness.
Or run a JDM CTR (PCT) ecu which is OBD2b spec and will PnP.

PROS: CKF bypass trick is noCan pass smog if CKF bypass trick is successfully performed in an integra or Civic Si chassis. If your Civic cx/dx is B-series BAR'd you should be able to pass smog too.

CONS: Requires OBD2b>OBD2a jumper harness; Cannot pass smog; speed limiter at 115-120mph.

Read more at http://honda-tech.com/showthread.php?t=1972711&kcplink=1