Car will not start after changing the fuel filter

I knew that after changing the fuel filter that I had a definite spark problem, my battery would not hold a charge. Then when trying to jump start the car, even after waiting several minutes to charge up the bad battery, it still would not crank up even with the help of starter fluid.

It took a couple of days to raise the funds for a new battery, but I finally got one installed. Now I can still hear the fuel pump prime, I even removed an alligator clamp from one of the fuel line very near the injectors to check fuel flow. When I had a friend turn over the ignition, without the help of starter fluid, I observed a steady flow of fuel into the clear container I used to catch the expelled fuel. After reattaching the fuel line, I then tried to start the engine with the help of starter fluid. The engine seemed to want to turn over, it would start to almost run, but it sputtered a little and stopped again.

Do you have any suggestions, and/or advice on where I should look or do next. All your help is much appreciated in this matter.

I mis-spoke earlier, it was the in tank fuel pump, not the fuel filter, that I replaced. Does that change things?