I have recently done an auto to manual swap on my 1998 Honda Civic hatchback. It came with the cvt transmission. I have not swapped out the auto ecu, the car has started and is running but it runs very rough and the check engine light and flashing "d' indicator light is on.Also, it has a slight surge and is trottling a bit high. How do I fix this? Does anyone know what modification I can do to the ecu to solve this problem?

 

Whenever the battery has been disconnected, it is normal to run rough / uneven for several minutes until the ECU re-calibrates.

You will have to swap the ECU to get rid of transmission codes. OBDII ECU's don't have jumper mods like OBD1 do.