The 3.2 Manual ECU does run a different Map over the 3.2 Auto ECU, but as said it will run on a 3.2 Auto, 2.6 Auto and Manual ECUs, but and from experience there is a but, without the correct Manual 3.2 ECU or at least getting a 3.2 Auto Tech 2 to a Manual configuration, there is a chance you wake up one day and find the car will refuse to start due to weird Fault Codes, which basically means the ECU can't see the Auto Gearbox.
That is to say, that the ecu 3.2 can execute a time in manual without problems until it fails or is there ecu 3.2 that despite putting it in manual with Tech2 after a while it will fail?
Sorry if I have not understood it correctly from the translator
Zirk is saying you
may have problems running a manual with an auto ECU, but if you configure it to manual with a Tech2, all should be fine. And vice versa, I'm guessing.