I don't have an SPI but, I do own an MPI and have looked recently at the emissions to resolve an issue (it was the Lambda sensor...).
The workshop manual linked above (the big 372 page manual) on pages 39 and 40 gives the specs for the SPI in manual and Auto forms. I don't see any difference (quick look) between the two and both ECMs are listed as MNE101350.
In the electrical and circuit diagrams pdf, pages 20.3 and 20.4, I see one extra MEMS input for the auto and that's an automatic inhibitor switch which must be to stop you trying to start the car when in drive. It removes the earth for the starter relay if the auto box is in gear. The manual wiring shows a permanently connected earth to that starter relay so, that MEMS input (105) would be unimportant.
You should check all of this but, I don't see any reason from the above that would stop you using an auto MNE101350 on a manual - they have the same part number, it appears, so should be the same.
Can you tell everyone the readings from your tester? This should confirm which sensors are working correctly - for example, if the Lambda is always one voltage and not fluctuating then there is an issue.
Good luck, Chris