The pieces of this puzzle are not fitting together. Can you provide some more detailed description of exactly how it acted/sounded at each step in this process?
The car had pressure at the rail but would not start, but then started after you replaced the fuel filter?
It sounds like it was flooded. I would suspect the fuel pressure regulator based on what I know so far.
Second suspect would be the crank position sensor as those tend to mysteriously come and go when they are failing.