Then something else isn't right...
The Idle should be 650 with the jumper in, so that the ignition timing can be checked/adjusted... makes sense to me.. and it states to check this first anyway..
As you probably know, when the fan kicks in, the idle speed goes up... and the TPS idle switch is obviously connected somewhere... so this could be one reason why your idle went up.. (just guessing here)
All the settings are base settings anyway... once the jumper is out, the ECU will take control over everything..
I agree about swapping TB's etc, but the manual doesn't take any of that into account
As Mazda made it, they should know how to adjust it..
I remember a thread a while ago on this subject... and don't really want to go down there again..
John