Maybe this will help....
joshoisasleep, maybe this will help. Maybe it's just basic info that you already know but just in case I figured I'd put these photos together for future reference.
If you think you have air in your injection system, which I'm pretty sure you do now that the fuel filter was disconnected, you will need to properly bleed the air from it.
If you want to rule out the possibility of bad fuel in your tank you can remove your fuel filter and drain it. Pour fresh fuel in the filter before putting it back on. This will usually be enough fresh fuel to get it started. If you want to completely isolate your fuel tank disconnect the fuel pickup hose on the fuel pump and stick it into a container with fresh fuel in it. (2 liter bottle, etc.) It's the red hose in this photo.
Then you need to start purging the air from the system. You do this with the primer pump. It's a manual hand pump on the fuel pump. Circled in this photo.
Just unscrew the plastic handle a few turns and the hand pump will free up so you can use it.
The next step is to bleed any air from the fuel filter. To do this open the bleeder valve on the filter and use the hand primer pump to fill the filter with fuel until it's squirting from the bleeder. The fuel filter bleeder is circled in this photo. Some years look different but they are all the same principle.
When bleeding the fuel filter it's just like bleeding a brake line. It should be tightened closed with pressure on it. You should feel resistance on the hand primer pump while closing the fuel filter's bleeder.
You can try starting the engine now. If it doesn't start then the next step is to bleed the injection pump. You use the manual hand primer pump and pump it until there's nothing but fuel coming from the bleeder. If there's any air bubbles or "spitting" keep pumping until there's a steady stream of fuel. The injection pump bleeder is circled in this photo. (sorry about the poor image quality)
Your engine
should start at this point after a little cranking. Once you get it started if it's running rough you can bleed the air from the injection lines one by one. You do this by opening the 17mm nut on the injector just slightly. Just enough to left fuel out. The fuel is under extremely high pressure, so be careful to keep exposed skin covered. The engine will stumble and run rough while the injector is open slightly. Just let it run that way for 20-30 seconds on each injector. (Only work on one at a time.)
Follow these steps and your fuel system should be properly bled. If it doesn't fire up and run smoothly then you've got a mechanical problem of some sort.