Stick your 14mm tool of choice on the end and break the torque. Once you do that you should be able to unscrew the rest with your fingers. When you pull the sparkplug socket out of the hole, the plug will be stuck in there. If you're simply inspecting your plugs and plan to reuse them, be careful not to bash the electrode against anything solid.
Now move on to plug #3. The boot comes out easily if you bring the top end towards you slightly. Route it out of the way towards the right side of the bike and remove the plug the same way as the first one.
Cylinder #2 starts to get a bit trickier. To pull the boot out, orient it the way I have shown in the picture. Also check to make sure that the plug wires you've already removed aren't getting in the way. If you find yourself getting stuck trying to remove the boot from the hole, chances are that's why. There are also a few other rubber hoses under there, make sure you push them out of the way if they are interfering. Once the boot is out, again route the wire out the right side of the bike along the fan shroud. Plug removal is the same as the rest, although a longer wrench may be handy.
Now for the hardest part... cylinder #1. This guy can be a bugger simply because access is restricted the most. The boot can be hard to get off because you can't reach. I found the easiest way was to stick my hand in upside down, reach through the "tunnel", and pull it up. Once you have it loosened, you can remove it from the hole from the left side of the bike. In the picture below, it's resting on the radiator tube, but there's plenty of room to pull it out further so you can get access. If you simply can't get the plug out and need more room, it's a piece of cake if you unbolt and/or drain the radiator to give some more wiggle room.
To get the plug removal tool in, still working from the left side of the bike, slide it in the tunnel "top" end first (so the rubber grommet is facing you) past the hole (so that you can utilize the hinge) and it will easily go in. I broke the torque from the left side of the bike by pushing the radiator hose out of the way and using an open end wrench.
Step four: Installation
Now you've got all your plugs out. Pat yourself on the back and open another cold one (unless you plan on riding when you're done). Installation is pretty much the same thing in reverse. Start with cylinder #1 and work towards #4. Stick your new plug into the socket and feed that towards the plug hole so that you don't drop it in there. Be careful not to smash the electrode against anything hard. Once you get the plug down the hole, tighten it BY HAND until the plug seats against the head. DO NOT use ANY tools to tighten it until you are 100% positive that the plug is fully seated against the head. If you crossthread your head don't complain to me about it. I warned you. Now that you double checked the plug, it doesn't take much to properly torque the plug. Each plug should have a crush washer on it, so all you have to do is "snug" it in there with the wrench. Don't make it gorilla tight. If you decide you want to do it by the book and can get in there with a torque wrench, good on ya. If you snap your plug or strip your threads by overtorquing it with a 1/2" torque wrench, it's your own damn fault.
Hopefully you've properly installed plug #1 by this point. I found it easiest to put the boot back on from the left side of the bike. When you get the boot down the hole, you need to firmly press down on the top of it to seat it. You'll hear it clicking into place on the top of the spark plug. Then push the rubber moisture seal back into place around the top of the hole and get ready for the next plug. Keep in mind that it takes me about as long to do cylinder #1 (the left most side of the bike) as it does to do the rest of them combined. So if you find yourself getting frustrated, relax for a bit and cool off before you break something, take a look at why you can't do what you're trying, and figure it out rather than trying to force it. Maybe you twisted a plug wire around 360 degrees and it's now not long enough. Maybe a vent tube is in the way. Maybe you're trying to put the wrong wire in the wrong hole. Or maybe you're using my guide but in fact aren't working on an FZ6, who knows. Analyze the situation and find a solution.
Cylinder #2 I found the most difficult to reinstall the boot until you know the trick. If you orient it the way I have shown below, such that the wire can slide through the upper tube (top arrow) and fan shroud (bottom arrow), it'll go right in. Go slowly and don't force anything. I have no idea what's required to break one of those plug boots, and I don't want anyone reading this to find out either. Also make sure you're putting the #2 wire back in the #2 cylinder, otherwise it's going to be a struggle. Fortunately they're labeled from the factory.
#3 and #4 are super easy, and you should have the hang of things by now. I've done the job several times now and it literally takes me about 20 minutes start to finish. Your times may vary of course, but hopefully you can see now that it's not such a daunting task after all.