Final update. I fixed the problem.
The issue turned out to be inside the ignition switch. Grey wire that goes to pin 41 on the ECU broke of from the soldered down contact. I re-soldered the wire and it all works now. Still not sure what it does, but I think it told ECU to cut the fuel off because ignition is not there. This info should have been in the manual in the Fuel Pump diagram. I also noticed that my FI light now worked properly as before it only worked in diag mode, but now it lights up solid because I had air intake sensor disconnected.
Unfortunately, I took many things(gas tank, ECU, Relay box, untaped many harnesses) of the bike that were not necessary. This grey wire and its behavior is not described anywhere besides a small table on the wiring diagram and even there it does not specify what to expect on this wire. After fixing it I measured about 9V on this wire.
Another interesting finding. 2009 CA specific V wiring diagram is described in the 2010 manual. To this date I could not find 2009 specific manual for my bike, so I will stick to 2010 in the future.
Another observation, bigger connector on ECU on 2007-2008 has 34 pins(according to the manual), but my 2009 CA specific has 26 pins matching the 2010 manual.
I hope this info will help somebody in the future. And again thanks for all your help.