I just finished the swap in my Integra along with in my CRX.
If you have a CRX then you do not need to drill the hole for the cltuch cable, however on a HB or Sedan 4G Civic you do.
You need:
Tranny
Pedals
Shift Linkages (Shift Lever)
Clutch Cable
Clutch Kit
Flywheel (if keeping the D series)
ECU
Gauge Cluster
Shift Knob and Boot
If you are doing the swap tyou have to rewire some shit as well... such as the reverse lights, nuetral safety switch and key release mechanism...
Ill check my CRX to actually find the colors for you if you like.
If you want to swap to a manual with the D series, go for it, it saves work down the road, dont listen to those who say it isnt worth it. But if you are swapping, Id wait til you had the motor.
Good Luck
Brian