If the ABS is from the original car, which is manual, then the ABS is not the problem.
The problem is in the ECU that is broadcasting that it's for an Auto. Meaning you didn't sort it right.
On ME7 CWGC needs to be changed, I've not looked at MED9.
As per prj, you cannot just "swap" transmission without re-calibrating the firmware as tonnes of little things won't work properly (even if you butcher all the CEL's which you shouldn't need to do if you do it properly!) and it will always be a horrible car to drive. There are so many subtle things I cannot be bothered to list them all but some of them are show stoppers imho. You need to do this properly as per factory would for a good driving, reliable car.
The engine ecu broadcasts a CAN message of how its operating and that includes manual or automatic so if you've NOT done this conversion correctly the other modules which have dependencies on them will get upset. It gets even more complex on later cars as you then need to perform proxy alignment too but that's a whole different subject..