Most Auto Ecus have a jumper at RP11 and have a blank space at RP12. Move RP11 to RP12 and you now have a Manual ECU. Here a closeup of the JDM Jumper configuration: Auto Jumpers

R96, C49 and R82 seem to be related to some Auto trans controls but can be left in place.

Some ECUs (Like the JDM P13-900) have resistors in both places. You can just remove both of them and replace RP12 with a jumper wire.

This applies to all ECUs that share the same board (P11, P12, P13, P14 and P39)