What is contained in this page will be information related to doing a motor swap on a EF(88-91 Civic).  This swap will only be specific to JDM B16A 1st gen motors.

So here we go:

Maintenance Items:
Gaskets Head gasket = US '94+ DelSol VTEC
Valve cover gasket = US '94+ DelSol VTEC
Spark plug O-ring gaskets = US '94+ DelSol VTEC
Intake manifold gasket = US '94+ DelSol VTEC
Exhaust manifold gasket = US '90-7 Integra or US '94+ DelSol VTEC
Spark Plugs = Any US B series motor
Cap and Rotor = US '90 Integra
Spark Plug Wires = Any US B series
Thermostat = US '90-1 Integra, US '94+ DelSol VTEC, '99+ Civic Si
Timing Belt = US '94+ DelSol VTEC
Water Pump = US '94+ DelSol VTEC
Lower Radiator Hose = '91 Integra
Upper Radiator Hose = Universal, may need trimming
Alternator = '90 Integra
Oil Pan = Any US B series
Oil Pump = 94 DelSol VTEC
Crank Pulley = Any US B series
Clutch = US '92 Integra GSR
Pressure Plate = US '92 Integra GSR
Pilot Bearing = Any US Civic/Integra
Throw-out Bearing = US '91-2 Integra, P/N 22810-ps1-015 $47.05
Flywheel = Any US B series
Axles = www.raxles.com, can use others, but best solution.
Intermediate Shaft = US '94+ DelSol VTEC
Mounts = www.hasport.com
Shift Linkages = www.hasport.com
Headers = best to use JDM B16

Wiring Information:
http://b16a.honda-perf.org/wiring.html
http://b16a.honda-perf.org/theswap.html 

AC Information:
Brackets from www.hasport.com or www.placeracing.com.
Belts = you will have to test and try out different ones.  Generally is shorter than original D16 belt.

Things I've learned:

1. If you use a HASport mount kit, be sure to follow instructions, specifically make sure you hammer a notch for the radiator.
2. Make sure the wiring for the O2 sensors aren't backwards.  99% of the time, most people will just add the one wire for the second O2.  What you need to do is flip the two... you would think it doesn't matter, but it does.  Car ran bad when it was reversed.
3. Do yourself a favor and get an 8 mm punch to take out the "bitch pin".  This is the pin that holds the shift linkage to the tranny.
4. Be sure to ground the engine after the swap, or else the car won't start.