The valve on the bottom of the filter is the water separater.
There is a screw by the primer pump that you loosen after you pump it up. So pump it up untill its tight then open the bleeder at the top. then repeate untill fuel streams out.
is the bleeder a black plastic lookin screw?
The bleeder screw is on the top of the filter housing by the silver thing that you pump.
If you ran it out of fuel, you could have some contaminated fuel. Here is the steps to remove water from the system. You may want to replace the filter also.
After you pump it up and bleed it till all air is out. You crank it over. Then prime it and bleed it again. Then crank it some more. Pumping the pedal wont help much, try holding the pedal 1/4 way down.
Let me know what happens