OK so if anyone is interested, that was air in the fuel system indeed. All it took to fix was simply trying to measure the fuel pressure, apparently this removed extra air and the bike started fine. Except of few scratches on the frame made by the falling tank, it's as good as new.
It's been 7 months since I have last ridden my FZ6 S2 '2009, and the battery was all dead. I quickly tired trying to kick start it, so decided to jump start it off my car. I unscrewed the tank and "rotated" it to get access to the battery, jump started the bike, let the engine heat properly, it...