Just from the sound of it, I would doubt if the rot were truly as isolated as you think. Usually if you get it in one spot, it is in others too. Usually, I prefer to replace rotten sections. This usually occurs at, or near the outside corners with a gooseneck. All joints should have a piece of lead flashing countersunk flush to the bottom of the gutters and bedded with roofing tar. I have always used lindseed oil for the treatment of wooden gutters.