Just to clarify, the spin on fuel filter has a water separator at the bottom of it that you had to reinstall from your old filter. Should be black, hard plastic i think. It has a collar on the bottom that will slide up and down and fuel/water will drain out of it. That's not what you should be trying.
The lift pump is engine driven, mounted directly to the block, below the filter, beside the fuel pre filter/heater. It should have a black rubber boot on it that points toward the driver's side frame and fender. It will likely be very stiff to push. Can often take a couple dozen pumps to prime an empty filter.
As mentioned by EKlem, you can loosen the screw on top of the filter assembly to aid in priming the system by letting air escape past the filter so it will fill more easily. If the priming is working, you should be able to hear a very faint high pitched whistle from the top front of the fuel pump each time you depress the lift pump to let you know when fuel has gotten as far as it should. It shouldn't whine until it is primmed.
I once spent over 40 minutes priming and cranking trying to start my truck. Ran the batteries dead cranking, had to jump it just to keep cranking. Even ether wouldn't get it running. Also tried using an air compressor to pressurize the tank and fuel lines. Was thinking it wasn't going to start but it finally did.
Eventually, my truck didn't start at all after several hard starts just a couple months later. Replaced the lift pump and overflow valve and haven't had those starting problems anymore. After you've tried everything, including making sure the tank has fuel, you may want to start by replacing those two parts.
Many say these mechanical lift pumps are indestructible but i know from experience that they sometimes need to be replaced. You could also try running a fuel line directly into a can of diesel with a cheap electric fuel pump. Likely won't put out nearly as much fuel as it should but it might give you hint as to whether or not parts are failing you. You could also try filling the filter and see if that helps it start.