Re: NL Idle vibration
Yes, your idle will be too high, and also your IAC solenoid will try to pull the idle down all the time. You will also experience harsh downshifts into first gear when slowing down, so I wouldn't touch the idle settings just yet.
Considering all you have done already, if you have a vibration ONLY and no misfire, I would suspect engine or gearbox mounts or a cracked flywheel, as suggested by Raven, but you seem positive they're OK and you mention misfire, so...
The MAF sensor does NOT influence the way a car idles at all, when it's dirty you'll notice your car seems slower than usual picking up RPM during acceleration, so I don't think this is your problem.
My next step would be to check for carbon build up inside the IAC valve and the throtle body, which is a very common problem with our crappy fuels and will give an air restriction at idle (idle too low). If this is the problem, once you get rid of the carbon don't forget to disconnect the battery for at least a couple of minutes to reset the KAM (wrong idle settings stored, etc) If this isn't the problem I'll be checking the intake manifold gasket for leaks. Spray some carby cleaner around the gasket area and look for idle quality changes (up or down)
Hope this helps, cheers