I have the identical truck. 92 7.3 NA
Mine sat for at least 5 years before I got it. And it took me a while to get mine started, as well.
You need three things to get these trucks started. Fuel. Air. And compression.
You are getting fuel at least as far as the filter. I would bet that you are getting it all the way through. But the simplest way to be sure is to crack the lines at the injectors, and watch for fuel at each injector. It doesn't pour out of there. It kind of dribbles.
If you are getting fuel at the injectors... Remove the glow plugs and do a compression test.
You are obviously getting air, with the air filter housing off.
Now here is where I amend the rule of three.
You also need two more things, to get these trucks started...
It has to be warm enough. GPs have to be working, or block heater has to be working and be plugged in a couple hours or so before start.
And... Speed. As in, the engine has to be turned over fast enough.
This last thing is what caused me to take so long to get mine started.
I had batteries that seemed good. The took a charge. They turned the engine over at what SEEMED like an adequate speed... etc.
The day I got it started, I finally decided to just hook up another running vehicle with jumper cables. (A CAMRY, no less. Tiny car, tiny battery.)
Let the camry run on high idle for about 20 minutes, while hooked via the jumper cables to the truck. Then run the throttle up a bit more, while trying to start the truck.
BAM!! Started right up!!! For the first time since I got it home. I had been working at it for well over a month, I think. And all the stuff I had done to it probably contributed to getting it started. Pretty much the same stuff you have done. So none of that was wasted effort. But yeah, just getting it to turn over FAST enough, was what got it started the first time. I put brand new batteries in it, and eventually a new alternator... And have not had that problem since.
One last... You said new fuel filter... How about the fuel itself? And if all else fails... You can pop the top off the IP, and check that the governor isn't stuck. Mine was making the clicking noise, but the governor was stuck. I took the top off. Moved the governor with my finger. Back and forth, until it moved freely on it's own, and returned freely when I moved it and let it go.
When you are done with everything, and have gotten it running... Fill that filter with ATF. Run it until the ATF has filled the injectors, turn it off, and let it sit for a while. Overnight. A week. Whatever. That will help clean out the injectors, and the IP and the lines as well.