First thing I would do is get a new filter.
After that I'd check the spray pattern on each of the injectors. Bentley has the procedure, but basically it is pull injector out of runner, stick in glass jar, run fuel pump (ignition on, lift sensor plate) and check for nice cone shaped flow pattern. Since you are obviously getting some fuel through, I would think the issue is at the non-functioning cylinders. Since it is likely fuel, I'd start with the injectors. If you find any that aren't flowing normally, you can either have them cleaned or there are a couple of people that have had success using carb cleaner and compressed air (very low PSI).
Note - I've had a couple of instances on track where the engine was starved for fuel without any issues - air isn't a problem as the fuel system is not a closed system. Gunk in the filter on the other hand is a problem.