Guessing Ken figured it out by now, but in case anyone else reads this thread, here are the directions:
There is a fuel shut off just above the water separator which you closed (and cleaned the separator while you were at it).
Remove old fuel filter and put a film of clean fuel on rubber seal of new filter.Tighten the filter quickly until it contacts mounting surface and then tighten by hand an additional 1/2 turn only.
Open the fuel cock by the water separator.
Loosen the air vent plug on the fuel filter 2 turns.
Turn on the key switch and wait for about 1 minute (let fuel bubble out, this is how the tractor fills up the fuel filter itself).
Tighten air vent plug.
Set throttle at minimum speed and turn the key to "Start" position. Do not hold key switch at start for more than 10 seconds continuously.
If the engine doesn't start try it several times at 30 sec intervals.
Accelerate the engine to remove any remaining air.
If air still remains and engine stops repeat above steps.
Mine started right up, but I am guessing from what lugbolt said that it would be important to make sure separator filled fully and then the fuel filter also.