Normally when the pump has primed the rail by turing the ignition on, wait for whirring, then turn off, the fuel rail should remain charged at 60 psi for a very long time. Mine stays 'charged' for hours. That tells you the pump is delivering the pressure. Using your toothpick the fuel doesn't just flow out under gravity, it squirts out at 60 psi until the pressure drops. You can sometimes get this if you break the QD's too slowly.
No you shouldn't be cranking the engine, anyway the fuel pump won't prime again until there is rpm - ie the engine has started.
At first I wondered if you had got the flow and return swapped over, but since you rode the bike that's unlikely unless by chasing this problem you could have swapped them over? It's best practice to reverse the male and female ends on the flow and return so you can't do this.
Make sure that when both 1/2's of the QD are mated, the non return valve balls are lifted and there is actually a through path.
You are a bit blind because you really don't know if the fuel pump is delivering its proper pressure (around 60 psi). If it isn't, fuel will not return past the pressure regulator back to the tank so what you think is a blockage may be a faulty fuel pump or blocked filter - which still leaves open the possibility of problems inside the tank causing reduced pressure output from the pump. I made up a pressure test line using a Tee piece, small pressure guage, and a male/female QD so I could break a QD and insert it in the line. The fuel pump delivers pressure in excess of the fixed regulator in the rail and fuel continuously flowing from the flow side and returning back to the tank. When the injectors open they draw fuel away from the continuous stream.
Your work on the QD may have dislodged something which has traveled downstream, so that is still an open possibility, but It would have to be a pretty big lump of stuff to block the path through the fuel rail regulator.
Testing the fuel line pressure first could avoid going into the tank. Unless you can confirm the fuel pump delivery pressure with a guage is low, it sounds like you may have to go inside the tank for a look around.
At the point your bike started to act up, had you filled up with new gas?
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