It looks like you have a long enough stub of copper coming out of the fitting below where the lead was installed to just cut off the leaded section with just clean pipe sticking up. THen, I'd install a no-hub connector (you'll probably have to go to a plumbing store to get the right sized one) and build it back up with pvc or abs (whichever is typically used in your area). THe only reason to keep it all metal would be if it were required, which probably isn't the case (it can be a requirement on high-rises and in some union friendly locations). Keep in mind that the proper location of the toilet flange is on top of the finished floor and anchored through it into the subflooring. If you notch the tile before laying them, you shouldn't need to drill through the tile. THe flange should be tight on top of the finished floor with the rim supported by the finished floor (which means it must go under it).