So this weekend I put everything back together and it seems to be working! It was a journey though with three sheared off bolts (on the CVT) but I got there.
The only doubt I have now is that I can hear the starter clutch engaging with a sort of poom sound. I already had a small suspicion about the piston that I bought for it, because it is not a genuine Honda part (which is not available as a separate part). Later I saw that it fits a bit tighter on the hub of the starter clutch housing. There is an O-ring in between these parts. It is shown here:
https://www.newco-autoline.de/docs/IDS-SWRA-starting%20clutch%20piston.pdfWhat causes the sound is probably a stick-slip effect at this interface. So you hear it every time you drive from a stop. Not sure if it's a problem, we will see what happens! Maybe its just because its new.
Edit: next day the sound has disappeared