There are so many reasons resolution could be limited. The most obvious is that signal does not increase proportionally to the number of observations (iirc signal = sqrt(# observations), hopefully someone else better steeped in the underlying theory will chime in). So adding n more particles does not mean you have n more signal and correspondingly more resolution. Run a reslog analysis to see what the expected resolution should be of 100,000 particles vs 40,000, and decide if they make sense. If the relationship is linear, you just need more particles. If it’s a plateau, something else is going on that’s limiting resolution.
It’s also possible you have variability or compositional heterogeneity that is limiting your resolution - the place to start there would be a 3D variability job, and simple volume series display, to get an idea about the magnitude of any flexibility or heterogeneity. You may need to sort those to get increased resolution.