Hi ca18ke20
The blacktop auto ecu will be ok. When you change to a manual gearbox you can disconnect all of the auto trans connections except for the neutral start switch (NSW) which is pin number 22 on the 22 pin plug.
This table (from club4ag) shows the manual blacktop ecu pinouts.
This is a table showing the pinouts on an auto ecu.
Hope you you find this useful.
Regards,
Peter