curo72

Something you can do that will definitely nail down that it's a fuel issue is pull out the fuel pump fuse and spray carb cleaner into the throttle body while someone else cranks the engine over for you. You'll have to spray quite a bit, but if it runs smooth you'll know where to look.
That said, it does indeed sound like a fuel issue.
Alternately, if you can get your hands on some noid lights, you could check to see if you have injector pulse at the cylinders that don't seem to be firing.
One more thought:
If it is a fuel issue like you suspect, do what jakemkz said, or you can follow the fsm in the electrical section, page 296 (or at least on the pdf version it is) called trouble diagnosis for non-dectable items.