The 'misfire' may still be with the ignition system but can also be due problem with fuel delivery, vacuum leak and MAF sensor.
A failing MAF sensor may not necessarily give a fault code (internal problem with sensor assembly - cold solder or cracked board) but can give various problems. So let's see if we could eliminate it as the problem. Disconnect the MAF sensor and start the engine (preferably in Neutral and no electrical load). This forces the ECM to use default setting. It may trigger fault code P0100 (reset required). If the 'miss' goes away, problem could be the MAF sensor. Clean the MAF connector with contact cleaner and apply dielectric grease then restore connection.
You may have contaminated fuel or failing fuel injector. When you replaced the fuel filter, did you observe the color of the fuel? A yellowish-orange color indicates corrosion in the fuel tank. Have you done a 'click' test of the injectors (use a mechanic's stethoscope or a long screw driver to check injector operation)? Check the resistance of the injectors, 10-14 ohms.
We can just assume the plugs and coils are good. So check the condition of the harness and connector then use contact cleaner to clean each coil connector followed by application of dielectric grease. A poor grounding may also affect ignition coil and injector operation. Disconnect, clean then reconnect the main engine harness ground points (2 ea. located near the intake manifold, close to cylinder #2).
You may also have vacuum leak or leaky intake manifold gasket. Use a carb cleaner and spray on those areas while engine is running and listen for engine response.
Though the CEL is off, there could be ghost codes. Get a free scan from Autozone.
Below is a copy of the 99 Maxima FSM, Engine control chapter. You can look into the diagnostic troubles codes related to you misfire problem.
http://www.nicoclub.com/FSM/maxima/1999/EC.pdf