First, if you paid the dealer to do all that work and the problem hasn't been fixed then you owe it to yourself to take it back to them and tell them you are still having the same problems. It looks like they can't really figure it out as they have basically given it a tune up with new plugs and wires, fuel filter as you mentioned but it sounds like they can't really pinpoint the problem or maybe they couldn't duplicate the problem when they worked on it.
Have you put a fuel gauge on it to see what kind of pressure you are getting? I'd tape it to your windshield (be careful *my disclaimer*) and see if you are losing pressure as you give it gas.
When you say you can't start the car in neutral, are you getting it to crank over or is it doing nothing at all? You could have a neutral safety switch problem if it's not even trying to turn over in neutral.
Lastly, try wiggling the connector slightly (not too much that you break it

) on the mass air flow sensor and see if you can get it to cut out or act up at all as you are wiggling it with the car running. Could be a number of things but you can start with those if you are mechanically inclined. PM me if you want.