People have tried the swap on the obd2 loom and have run into all sorts of problems. You're best of swapping the loom completely if you have the skills to do so.
Hello,
I have had the same problem and after loads of phone calls to Mazda HQ i found out that each year for the mx3 v6 they changed some of the colours of the wires.
The bulk of the wire colours are correct however there are a few that i have had to open the wiring loom to trace.
With regards to the factory manual, make sure that your VIN is covered in the manual that you have as there are different ones.
Some of the manuals have red covers, some have blue and there is a rare one in green, as told to me by Mazda HQ.
I have seen the red and blue however mazda never allowed the green out of there sight.
The only other option i can think of would be to obtain the microfiche for your car.
Thats what i have done and i use them at the library to get information and printouts.