Mark Sam:  You have been given very good advice by people who appreciate your Family Treasure.  There is No Way your Grandfather's Krag should be made to look 'New' like those idiots on "American Restoration" do to legitimate antiques.  Your Krag is something that has been entrusted to you.  It is for you to enjoy for a time, but it will be here after you are gone.  "Do Nothing" is sound advice.  This Krag has changes that were done by your Grandfather out of necessity (i.e. incorrect replacement sights, front stacking swivel & handguard removed, receiver ring dove-tailed for now missing sight).  You have a rare Krag that was altered by an ancestor (A beautiful thing).  Keep it as is!  Maybe, obtain correct missing parts just to have them.  You can clean the bore.  Attempt to wipe off paint spots on wood with soft cloth and mineral spirits or turpentine.  Use a pick and toothbrush, as Mr. Hosmer suggested.  You can put some moisture and luster back in the wood by hand rubbing with linseed oil or linseed oil/turpentine mix.  You can wipe down metal parts with Hoppe's #9 to clean off paint, dirt, surface rust and dried 'gunk'.  You can protect the metal by wiping on RIG (rust inhibiting grease).  The wood stock can be periodically freshened with a rubbing of linseed oil or "Pledge" spray furniture polish.  If the wood stock, action and bore are sound, take her out and shoot her!