Since your in Slovenia, it is the metric system for you...Each bottom cylinder gasket is 1.5875mm...Most YD-100s I know use 2 bottom gaskets so your equivalent bottom gasket thickness needs to be at 3.175mm before compressing it down when torquing the cylinder back down on top of them.
I am surmising your having to make your own gaskets in Slovenia.
yes you can see a little bit of the piston... If i understand correctly its best that its not obstructing the port but the engine has plenty of power and revs up nicely.