So I have had my guitar for about 2 years, unfortunatly I have not paid attention to the cleaning aspects of the instrument. I did some small research on this. It seems possible to clean the fretboard using nafta. Is this something you would recommend and what type of oil or similar should I use afterwards? Should I oil it up a couple of times and letting it set not to oversaturate it? What do you Think? The guitar has a wizard III neck maple Wood.
Naptha is a cleaning agent you can use, but it's really only required if there's gunk you can't remove any other way.
We don't care much about the neck wood, but we DO care about the fretboard wood. If it's maple, it's likely that it's been lacquered/finished (even with a matte finish), so there's no point in oiling it. If it's a rosewood or ebony fretboard, you can use a bit of mineral oil on it -- just a few drops wiped on and wiped off. Never let it sit to "soak in."

Just to clarify -- you're not "conditioning" a rosewood or ebony fretboard with any of the products on the market today. You can let your fretboard sit for 30 years without ever putting any oil on it and it will be just fine; there's enough natural oils in rosewood or ebony to keep the wood for several hundred years. The surface might look a little dry, but that actually doesn't mean much. You definitely do NOT want to let oil "soak into" the wood; you're not helping anything, and the oil that soaks in will eventually bleed out of the wood, which just gunks up a new set of strings.

Do NOT use real lemon oil on your fretboards (the "lemon oil" normally referred to is a "lemon oil cleaner" like Olde English, which is mostly mineral oil with some solvents -- and no real lemon anything. Real lemon oil is used in cooking. Real Rosewood oil isn't even made from the same tree as your fretboard and it's supposed to be used for aromatherapy. Never ever use it on your guitar). If you can find normal mineral oil, it's cheaper and just as good for your guitar as Fret Doctor and/or any of the other tiny-bottle goops that you find at a guitar store or online. Mineral oil is also sold as "block oil" for oiling butcher block and other wood cutting boards in your kitchen.