I'm late to this party but I don't think I saw this mentioned. Do you have pics of your bored out 13mm inlet? I'm betting this is what's holding you back. Boring out the inlet can be done in like a million different ways, and sometimes it's done extremely conservatively. Do you have any photos of it?
Ideally it should look close to the attached image, although this is pretty extreme. After the dremel or drill press, you need to use a round file to really open up the inlet and make the whole intake a round funnel shape. Pic from ciao nl attached. I've seen multiple scenarios where I got an engine that someone said was "bored to 13mm" and the intake patch was literally not tochhed at all. They just drove the drill bit down like 15mm and stopped. This creates a MASSIVE wall for the air and fuel to smash against (eddying) and often makes your engine worse off. You'd be better off not touching it at all. The whole entire thing needs to be opened up on the left and right. This doubles as a way to alter your intake timing pretty significantly as well. After porting my intake the intake duration is 168deg and I'm pretty sure vespas are typically like 150 or so stock? Someone correct me?
Anyways I digress. But yeah if you could provide some more details on how you did the inlet porting that would be helpful. Out of all the modifications you did I think this is the biggest wildcard as to top speed. The additional intake timing from correctly modifying the inlet is huge for high rpm ripping.