There is a
thread on Honda-Tech about this. The English is a bit hard to follow so I rewrote it here.
Auto to manual ECU conversion:
1. Disconnect the battery, negative terminal first.
2. Locate the ECU. It's underneath the rug under the passengers feet.
3. The Ecu is underneath a protective cover, which has 4 10mm nuts holding it in place. You will need to use a 10mm deep socket to remove it.
4. Unplug the harness.
5. Unbolt the Ecu from it's protective cover.
6. Remove the cover/lid from both sides of the ECU.
7. Locate the 000 resistor that is labeled RP13.
8. In addition, locate the target area RP14 on the other side of the circuit board.
9. Very carefully de-solder the resistor from RP13. Use tweezers or a small screwdriver to remove it while the solder on both ends is melted.
10. After successfully removing the 000 resistor from RP13, flip the board over and place it on the RP14 spot.
11. Re-solder both ends of the resistor.
12. Screw every thing back together in the reverse order of removal.
13. Put the ECU back in the car and reconnect the battery.
14. Start the car, everything should be good.
You do not need to keep the TCM connected or in the car after this. I would secure the end of this harness so it doesn't bounce around and make noise while driving.