You mean the pipe that runs to the toilet, this is called a lead bend, you want to replace this with abs or pvc pipe, new elbow and new closet flange, the way to do this is, right where the lead pipe enters the cast pipe you want to cut at least 3" from the hub of that fitting, this part of the lead bend is solid unlike the lead up to the toilet, by using a fernco coupling you can make the transition to the plastic pipe.
What do you mean: The copper pipe looks, would it be stupid to keep it.?
Clear hoses? You mean pex pipe?