And seven-time world champ Rossi had no answers other than to marvel at Stoner's pace and hope that his Yamaha team can find some solutions, although he expects the next big change for his M1 to be at Brno in August.
Stoner is bristling with confidence and says the small changes to Ducati's engine management electronics, which allows him more precise throttle control, is proof that earlier theories that he had lost confidence were wrong.
"I hadn't lost my head as some people thought and with these small changes I can ride the bike the way I want to," Stoner said.
Based on today's performance, the 26-lap race here is going to be hard work for everyone bar Stoner unless someone brings a new game to the table.
One rider unlikely to be doing that is Suzuki's Loris Capirossi who highsided heavily in session two at the fifth gear Ramshoek left-hander, with a footpeg puncturing a hole in his right forearm (although there was no muscle damage).
Capirossi was already riding with broken bones in his right hand, an injury
which forced him out of last Sunday's British Grand Prix.
AMA Superbike champion Ben Spies subbed for Capirossi in that race and is here at Assen as an unwilling spectator. The prospect of late call-up for Saturday's race, now with just two hours of practice and qualifying remaining, would be a difficult call for Suzuki and Spies.
Capirossi is undergoing surgery and is an unlikely starter with Suzuki having until just before Friday morning's third free practice session to nominate a replacement. Or none at all.
Suzuki's situation is made more difficult by the forecast of rain at Assen over the next two days at Assen, a track where Spies has never raced before.
And Suzuki's troubles run deeper with their other factory bike, ridden by Australian ace Chris Vermeulen, tenth fastest in practice and 1.1s away from Stoner's Ducati.
American John Hopkins fared little better with Kawasaki's troubled ZX-RR and finished the day eighth, and still outside last year's lap record which took such a hammering at the hands of Stoner.
