From EB's FAQ section:
How do I maintain the neck on my new Music Man guitar?
Since the neck is unfinished, it can be more susceptible to humidity changes. An annual (or so) dose of gunstock oil will help to keep the neck maintained; we use and recommend Birchwood-Casey Tru-oil, but any good quality gunstock oil will work.Clean the neck first. Use a small amount of Tru-oil, leave it on for 5 minutes, then wipe it off with a paper towel. After that, apply Birchwood-Casey Gunstock Wax. Be sure to douse the paper towel with water before disposing of it! Read the wax and oil manufacturer's instructions regarding disposal of these used paper towels.
Birchwood-Casey products are available at most sporting goods or gun stores, or now you can order them direct. Their web address is http://www.birchwoodcasey.com.
Rosewood fingerboards should not be treated with the gunstock oil; instead they should be treated with a high grade of lemon oil, or even better, with Ernie Ball Wonder Wipes Fretboard Conditioner. These wipes really work.
For cleaning, try using the same high grade of lemon oil to clean the entire neck, both maple and rosewood fretboards, and again our Wopnder Wipes Fretboard Conditioner. If the neck is very dirty, you can use a small amount of Murphy's Oil Soap, diluted 3:1, to clean it. Keep in mind that if the dirt has gotten into the wood, it cannot be removed except by sanding it down, which we do not recommend a lot of. It is better to keep it clean in the first place. Washing your hands first helps!
On an maple neck, some discoloration after many hours of playing is normal.