Having a similar problem with my Aerox 100. It is a 2002 model.
I have not done as much to it as you have, but I have gone to a Tecnigas RS pipe, and a Malossi variator, and kevlar belt. When I went to the new pipe, I found I lost nearly all the low end power I had with the stock pipe, it doesn't really make much below 6750 rpm, so I find I have a very narrow powerband.
That said, I have been chasing the top speed speed I used to have prior to making these changes. I used to do an indicated (not actual) 105-110 km/h in completely stock form. Now it seems I am maxing out at about 90 km/h. I have tried every roller weight from really really heavy to really light, and just cant get the results I expected. Also acceleration is a bit better, but again a bit disappointing.
In hind sight, I think the pipe I went with is a bit to agressive for the stock engine. I am curious if maybe the LeoVince pipe might be a bit better. I have never seen one for the Aerox 100 in person, but from the photos it looks like the shape is a bit shorter and fatter that the tecnigas. From what I know this should indicate it would be better at low rpms.
But as with you, the lack of top speed really has me a bit stumped.
I would love someone who has a really nicely setup Aerox or Neo to post their setup!