Thanks again for support. Good news !
Just done 5 complete flights with soft 3D without any major issue.

Here's the story (btw my soft is 2.8.0). I've checked all the parts, using the vibration analysis. Motor alone OK. Motor + main gear KO.
So after investigations (cannot do much more than replacing the main shaft and bearings), I decided to replace the 3M adhesive with a GAUI thick foam. The overall vibrations level (full set heli) is far better but still about 130. However doing a test flight gave...no problem anymore!

So I applied "standard" tuning (except for rudder servo delay set to 0), and everything's fine! The heli is quite nice to fly, of course I'll have to tune it a little bit more to get it closer to my habits but it's OK overall.

The only thing I noticed is that my tail servo is heating more than before (probably due to the high frequency), but still I can touch it without any injury.

Conclusion: the Spirit 2 is nice and good to fly. Your assistance was really helpful and I thank you for all.