There's a stop screw on the horizontal cylinder that will change both cylinders equally because it's linked. The screw is vertical and forward on the link. It has a yellow dot of paint to mark when it was tuned in the factory.
But they'll tell you not to touch it and that you need to do the adjustment electronically. However I've just been through this where mine was too low and I arced it up for awhile, to about 1200rpm to stop it stalling at lights. I turned it a whole revolution noticing exactly how I was changing it in case I had to return it to the original spot.
However stalling is what the 2004 ones used to do before they had the recall because they had weak closing springs.
When I checked mine I found one spring broken although it was of the later type so mine must have had the recall.
My Ducati service bloke told me that the recall is still current and available if the bike is in the system regardless of the number of owners.
So what I'm saying is if yours hasn't had the heavier springs fitted on the recall then it may have had the idle cranked up because it wouldn't idle properly with the thin springs.
Now that I've replaced my broken closing spring I have lowered my idle back to 1000rpm and it's fairly smooth so I suspect the spring may have been broken throughout my 9000K's of ownership. Is that clear as mud? I have a photo of that screw somewhere if you need it.
Thanks for the quick response! I have read about Service Bulletin 05-001 where the exhaust return spring and the ecu needed to be replaced. I am the third owner of my ST3 so I don't have any record of whether this service was performed. I was just about to ordering the parts but before I did so, I checked the part number on the ECU and it is the correct part number. It is quite possible that the springs were also replaced. I have a valve clearance check scheduled next month and I will request that the springs are checked to confirm that they are also the correct ones. If not, I will be certain to get them swapped out. I will look for the screw and if I cannot find it I will request that photo from you.