2003 Ford Windstar engine has spark will not start.

Engine Performance problem
2003 Ford Windstar 6 cyl Front Wheel Drive Automatic

I had the check engine light on and the code was miss firing in cylinder 3. I changed the plugs and wires and the code was still on and the van ran rough. Next I changed the ignition coil and it was bad because it ha cracks on the backside where the gel coating is. After replacing that the van will not start. The motor cranks over and sounds like it wants to start but wont. I tried severl times and the battery died so I went and bought a new one. Then I was thinking that maybe the fuel filter was clogged and not getting fuel to the motor. I changed that and still it sounded better when I tired to start it but still would not start up. I pulled a wire and checked for spark and it was a strong blue spark. The fuel pump turns on when you turn the key. If I pull the line from the fuel rail and check for gas to come out while trying to start it that should tell me that I am getting fuel to the motor right? Is there anything that I could have knocked loose when
I was putting the coil in that would cause the van not to start? Or could something else be wrong? Or ould it be a sensor or something along that line which is now not allowing the van to start? Anything would help thanks