The Australian's apparent ease at the front of the field belied severe chattering problem, which Stoner said forced him to ease off and allowed Yamaha's Jorge Lorenzo to close in.
With the planned post-race test at Estoril cancelled due to rain, Stoner says the team needs to hope for dry weather at Le Mans in order to work on the problem before Sunday's French Grand Prix.
"It was disappointing that the weather in Estoril on Monday prevented us from testing," Stoner said. "We need to work on the chatter issue we have on the bike so let's hope we have some dry sessions from day one in Le Mans so we can get out on track and work on it."
The phenomenon of chatter aside, Stoner said he was confident heading into Le Mans, particularly after winning at Jerez and Estoril - circuits he has not traditionally thrived at.
"The past two tracks have not historically been my best but I've managed wins at both of them so I'm hoping we can go to Le Mans and be competitive again," Stoner said.
"I've had some mixed results there in the past, the track layout is unique, it's a little stop-start with a lot of braking and I think this year both the Hondas and Yamahas will be competitive there."
Honda stable-mate Dani Pedrosa said he needed to improve his pace in the opening phase of the grand prix, having fallen away from both Stoner and Lorenzo in the opening laps at Estoril.
"In the past I felt comfortable riding [at] Le Mans, [and] had good results in 125cc and 250cc but not really in MotoGP, so I have something small inside me I want to achieve," the Spaniard explained.
"We've had three good races so far, I'm riding well, but I missed something in all of them, especially on the first laps, where I've been stronger in the past. I need to put everything together and if we get better starts, we will start wining races."