This topic is been covered a million times but hopefully I will be able to put on one page what I have gathered off the net and from experience with my swap.  I am not an expert and I nor Hybrid are  responsible for any problems that may arise from your swap endeavors.  DO YOUR HOMEWORK!!! and things will go much more smoothly.  This is my first tech article so if you see anything out of order, let me know.  Okay with that out of the way, on to the info...........

Groundwork 

To begin with, I will assume all of you reading this have bought a 96-98 OBDII complete swap, meaning; long block, tranny, ecu, shift linkage, axles, ect.  Doing so will make your life much happier and your swap much more easy.  There are other options like an OBDI or even the pre-OBD motors but it's not recommended and not legal in most states.  You should have a motor from a car that is the same year as yours or newer.  

Options

These are the recommended swaps that are applicable to this page:

1. 96+ USDM, JDM B18c1

2. 96+ USDM, JDM B18c5 (Spec R)

3. 96+ USDM del Sol B16a3

4. 99+ USDM Civic Si B16a2

5. 96+ USDM, JDM B18b (non-Vtec)

6. 96+ CRV B20b, B20z

What you'll need  

If you purchased the complete swap; motor, tranny, axles, ecu, shift linkage, wire harness, cat, then you are well on your way.  The EK is an excellent choice for swaps due to the mostly plug and play, bolt-in process.  Here are the parts you'll need to drop the motor in the car correctly:

Rear Tranny mount from the 99-00 Si:  50827-S04-N10    $40.46

Driver side mount bracket from the 99-00 Si:  11910-P30-000    $46.94

96 del Sol AC bracket:  38930-P54-000   $109.13  ( only if you want to keep your ac)

I bought these mounts from HParts.com    (updated 2/17/2007)

Wiring*

** The 99-00 Si engine harness looks the same as the 96-98 but the ecu plugs are different and the interior harness (green plug by the ecu) is pinned differently. You can swap the 99-00 Si in a 96-98 EK and use the 99-00 Si engine harness and ecu but you will have some problems.  I don't have experience with this swap.  I'd recommend staying with the same year/ generation motor as your car for simplicity.  A 99-01 B swap in a 99-01 EK is truly plug and play since the B16a2 came in a Civic**

Okay, this is the place where most people get overwhelmed but it's actually quite simple.  If you can install a radio, you can do this.  You'll need to remove the engine harness from the B motor.  I cheated and bought a 98 EX engine harness (5-speed) for $100 at a junkyard since all the Vtec wires were already there.  But if you don't want to do that then take your harness off your D motor and put it on the B motor.  You have to do this since the wiring for the EK goes through the firewall and to the ecu, unlike the two piece Integra and EG engine harness.  Now you'll notice that some wires don't reach the sensor, simply cut the plug and extend the wires where needed.  From memory I had to extend my primary O2 sensor only because my header has the O2 on the back of the header and not the front like the OEM exhaust manifold.  I also extended the wires for the  EVAP to mount it on the firewall.  The IACV will need to be rewired if you are using a CX or DX harness.  Just use the plug off the Integra harness (2 wire) and match the colors to the Civic harness (3 wire).  You will have an extra Orange wire that is unused, just tape it out of the way.  Next you have to move the wire at A14 to A12.   If you have the B18b or the B20b,z  then your wiring is complete.  Now comes the fun part, wiring up the Vtec and IAB (B18c1).  Cut the plugs off the B engine harness that came with the motor ( leave enough wire to splice) and wire to the D engine harness at the ecu as follows:

Vtec Pressure switch    C15

Vtec solenoid                A8

Knock sensor                D6

IAB solenoid   (B18c)    A26

There might already be wires at the ecu where you want to splice.  Just cut the wire leaving enough room to strip and crimp and connect the wire coming from the new sensors on the motor.  Tape off the other side of the wire since it was for the D sensors and won't be used anyway. 

Katman's EK pinouts:

96-98  here

99-00  here

Here are the EK (Civic) pin outs*:

DC (Integra) pin outs*:

Click the link to see the 96-97 del Sol B16a3 OBDII info.

Other wiring that needs to be address is the second O2 sensor,  the crank fluctuation sensor (CKF), the EVAP and the IAT.

The CKF plug on the D harness is a three wire plug, but on the B harness it is a two wire plug.  If you look at the two plugs, two wires match in color and the third wire on the D harness is a ground and not needed.  Simply swap the plugs by taking the plug from the B harness and splice it on the D harness.  Tape up the extra wire that wasn't used.

The EVAP purge solenoid valve plug is different so just splice from one harness to the other.

The IAT (Intake Air Temp) sensor needs to be extended if you use the sensor on the B motor.  I used the EX harness and an Si intake tube so I just used the sensor that was for the D motor.  No need to extend.

Last but not least, the second O2.  The plug goes through the floor board behind the cup holder. If you have an EX and are performing the swap, then all you need to do is plug the O2 to the plug behind the cup holder.  If you have the CX or DX then  look at the O2 plug from the pin side and then look at this diagram below and wire to the ecu.

(viewed from the pin side on the male plug)

For the 96-98 OBDII ecu:

1 (green) goes to D13 (green/ blk) for sensor ground 

2 (white) goes to D14 (white/ red) for sensor signal 

3 (blk/white) goes to A5 (blk/ white) for heater signal 

4 (blk/yellow) needs to "TAP" into A11 (yellow/ blk) for 12v power 

If you completed the above directions successfully, you will have no check engine lights when you crank up the car granted you used the 96-98 swap in a 96-98 EK.

**Also, after you have wired everything correctly, you can use the OBDI style ecu with an OBDII-OBDI ecu converter harness sold for about $250.  This is a popular option for performance reasons and to bypass the OBDII programs altogether but keep in mind the wiring needs to be completed for the Vtec to work correctly.  If you choose this option you can omit the secondary O2 and Crank Fluctuation sensor (CKF) since OBDI doesn't look for these signals.

The Swap

I'm not going to tell you how to do the swap.  If you can't figure it out on your own, take it to a person who knows how to do the swap or buy a Helm's manual.  You should have one handy anyway!!

Mounts

Driver side- Use the mount bracket I mentioned above.  This piece bolts to the block below the cam gears.  reuse the civic studs.  Also, use all  other civic parts at this location. (picture)

Rear tranny- Use the rear upper tranny bracket I mentioned above.  Use the stock civic rubber mount. (picture)

AC Bracket- Use the ac bracket I mentioned above and reuse the civic stud and rubber mount.  Integra piece is similar but won't work. (picture)

Front tranny bracket- Use integra piece on the tranny but civic stud and rubber mount.  Integra stud and rubber looks the same but won't work.

Upper tranny mount- Use all the civic pieces.

If you do keep your ac, there is no need to discharge the system.  Simply unbolt the ac compressor from the D motor before you take the D motor out of the car and strap it out of the way.  When you put the B motor in the car, with the correct ac bracket, bolt the ac compressor back to the motor.

Also, nothing else from the D motor can be used including the tranny, axles, ecu, shift linkage.  It won't work so throw it away.

Issues

Code 91- Low Pressure in Fuel Tank:  This only applies to USDM ecus.  I found a way to get around the code but isn't a true fix.  This only happens when the car has been sitting for a long time like over night.  You have to put the key in the ignition and turn it to the accessory position (radio on but the car is off) and count to 10 slowly then crank the car. That will pressurize the fuel lines and the code will not come on.  

Also, the exhaust will need to be modified. If you use the OEM exhaust manifold and the cat you will need to trim you b-pipe (middle exhaust pipe) a few inches so it will bolt to the cat.  If you use an aftermarket header, you can bolt your b-pipe straight to the header with out the cat but that wouldn't be legal.  :)   If you do use the cat, you will need to trim the b-pipe to make it fit.  Most experienced exhaust shops will do this for $30.