Wait a minute here; all you did was to replace the extractor, right? You did not replace the bolt block or anything like that, just the dang extractor. You were able to get the old one off and the new one on. The new one should fit smoothly opposite the bolt lug with the ejector channel cut - it does not sit on top of the raised rib on the bolt that is straight up when you go to reinsert the bolt into the action.
If the new extractor fits snugly/smoothly onto the bolt, that is that you cannot feel any raised edges around the body of the bolt where the extractor springs (the two round spring arms on either side of the extractor) that need smoothing then don't go at it with a file or anything because you most likely do not need to.
Sometimes Mauser bolts can be a pita to get back together but most often they go together easily. If you removed the firing pin from the bolt body then you need to take the firing pin with the spring on it and place the firing pin tip into one of those little holes on the round 2 hole pieces on the stock and push down with the safety block until the spring compresses and you can screw the safety block back onto the rear of the bolt - once you have done that you need to continue holding the spring compressed and reinstall the safety lever which will hold the firing pin back under spring compression and then the firing pin is locked back in place by the safety lever so you can then screw the whole thing right back into the bolt body. Once you get to where the safety block (or what the hay ever it is called) is flush against the bolt body, you need to depress the retention pin with your fingernail and turn it the 1/4 turn to lock it. When you go to reinstall the bolt to the rifle, make certain the extractor claw rides over the bolt lug opposite the lug with the ejector channel and that should do it for you. HTH.
