Having struggled with set-up issues throughout the weekend, Stoner never really featured in the battle for pole position and only salvaged fifth with a late improvement.
The Australian says he remains hopeful of finding overnight improvements, but admits his ambition at the Italian Grand Prix may be limited to simply trying to hang on to his works Honda team-mate and Yamaha's championship leader.
"This weekend we're just missing something, especially in the longer corners we just can't get the bike to turn," Stoner said. "We can't stop the rear chatter in the exit and in the end we can't put the lap together.
"We're losing some tenths in each sector, if we get the bike sorted for one sector then everything should come together easily but it's been a difficult weekend so far.
"We still have tomorrow morning to improve our set up and sort out a few of our weaker points, if we do then we might be in with a chance.
"I'm not too worried about second row, we'll hopefully get a good start, see what we can do and try to hang with the guys at the front, but honestly at the moment Jorge and Dani are in a different level."