If this turns out to be a Confederate rifle, cleaning or restoring it will have a very negative effect on value of the rifle. Longrifles in my experience, are a different story. With them, competent restoration will add to the value.
It takes many years for items like this have a lot of patina. I have seen many items including rifles, swords, and powder horns, that have had all of the patina taken off in a misguided attempt to make the item look new. I have been guilty of this myself before I learned better.
I would suggest you put it back together as is and take it to a knowledgeable Civil War dealer like Shannon Pritchard in Richmond for identification and value. Get a copy of North South Trader Magazine and you will find a list of dealers that can help you.
Best of Luck,
Michael