Well there are two thoughts here. It's your car and you should be happy with it. At this stage with it all apart it would probably easier to take care of the problem now. You did not go into specifics but I assume it is fixable. But how much will it cost. Most shops are familiar with how to fix smaller repairs that match extremely well.

On the other hand, unless your building a showcar, it may just be something to not worry about. Enjoy the car and know you gave it new life. You can always fix it later if it truely bugs you. My question is, would this be an issue any non car guy would notice? If it is, get it fixed now. If not, I am not sure I would worry about it. Some pics of the problem might help.