The 29-year-old is making his Suzuka debut alongside Michael van der Mark and Takumi Takahashi, winners for the past two years at the factory Musashi RT Harc-Pro squad.
But it is event rookie Stoner who has led the CBR1000RR challenge this weekend, clocking a close fourth best lap time in both Friday qualifying (+0.307s) and Saturday's Superpole session (+0.335s). That put his team third on the grid, behind Yamaha Factory Racing and Team Green Kawasaki.
The single-lap Superpole format was another brand new experience for Stoner, who praised the spectacle.
"In practice this morning I had a small problem with the rear brake and we only got one lap in before the session ended. We went from that straight to the pole shootout, which is something I've never really experienced but really enjoyed," he said.
"I think the Suzuka circuit puts on a fantastic show. Watching each rider do the entire lap is really something exciting for the crowd. It was a new taste for me.
"I felt a little bit nervous on the front tyre because we had so much more rear grip, but anyway the bike was working well and I'm pretty happy and satisfied with the lap time.
"We've been working all week towards a long race and to immediately turn around and do a good lap time is tricky. But it's only one Superpole lap and tomorrow we have 8 Hours of racing, so I'm pretty sure the other sessions have been more important.
"We've got a couple of small things we'd like to improve for the race. Everyone is in the same position of believing they can be a bit faster. But this is the thing we have to live with, with three different types of riders and three different styles, you have to try and find the best compromise possible.
"We've done a good job so far. Everybody is pretty hap py. It's going to be a long, hot race and we'll see what happens at the end."
Stoner also gave an insight into how it feels to be back at an FIM World Championship event, and what has changed from his MotoGP days.
"We're not really going into this race like I would in the past in MotoGP. That intensity has left me," he said. "It's a lot more relaxed atmosphere and this event has a more relaxed environment.
"You don't have the intensity of a sprint race of 45-minutes. This race is 8 Hours long and you have to work with your team-mates and the people around you.
"It's very different to what I'm used to and this is an event that I've had on my bucket list for many years. It's nice to finally be here without the added pressure these other guys have of being in the middle of their racing season.
"The only negative is, having such little time on the bike in the last three years, it takes a little while to get all the muscles and everything worki ng again."
Sunday's race starts at 11:30am.
Suzuka 8 Hours: Top 10 grid positions1. Espargaro*/Nakasuga/B. Smith Yamaha Factory #21 2m 6.000s2. Watanabe*/Yanagawa/Yudhistira Team Green #87 2m 6.287s3. Stoner*/Takahashi/VD Mark Musashi Honda #634 2m 6.335s4. Tsuda*/Lowes/Waters Yoshimura Suzuki #12 2m 6.516s5. Kagayama*/Kiyonari/Haga Team Kagayama #17 2m 7.990s6. Aegerter*/K. Smith/Hook FCC TSR Honda #778 2m 8.076s7. Yamaguchi*/Wilairot/Elias Toho with Moriwaki #104 2m 8.382s8. Nigon*/Deguchi/Izutsu Trickstar Kawasaki #01 2m 8.950s9. Uramoto*/O'Halloran/Herfoss Sakuri Honda #71 2m 9.409s10. Ogata*/Aoki/Konno Motomap Suzuki #32 2m 11.019s*Set the team's fastest lap in Superpole.
Superpole lap time by each rider1. Espargaro Yamaha Factory #21 2m 6.000s2. Nakasuga Yamaha Factory #21 2m 6.059s3. Watanabe Team Green #87 2m 6.287s4. Stoner Musashi Honda #634 2m 6.335s5. Tsuda Yoshimura Suzuki #12 2m 6.516s6. Lowes Yoshimura Suzuki #12 2m 7.144s7. Takashashi Musashi Hond a #634 2m 7.697s8. Kagayama Team Kagayama #17 2m 7.990s9. Aegerter FCC TSR Honda #778 2m 8.076s10. Yamaguchi Toho with Moriwaki #104 2m 8.382s11. Hook FCC TSR Honda #778 2m 8.472s12. Kiyonari Team Kagayama #17 2m 8.806s13. Nigon Trickstar Kawasaki #01 2m 8.950s14. Yanagawa Team Green #87 2m 9.006s15. Uramoto Sakuri Honda #71 2m 9.409s16. Wilairot Toho with Moriwaki #104 2m 9.877s17. O'Halloran Sakuri Honda #71 2m 10.391s18. Deguchi Trickstar Kawasaki #01 2m 10.771s19. Ogata Motomap Suzuki #32 2m 11.019s20. Aoki Motomap Suzuki #32 2m 11.681sOnly two riders from each of the top 10 teams participate in Superpole.
