So, I "fixed" the intake boots with epoxy and rtv. Started the bike and it ran smooth, idled nicely at around 800-900 rpm, I stoped it and started it a few times and it was all the same.
Decided to test my charging system, and then it all went downhill, when I revved the bike to around 3000, the revs just stayed there, so I'm guessing the advancer was closed before (during the starting and idling) and once I gave it some gas it opened up and didn't close again.