Welcome to the Community Ando:
Yes, I would take the copper out and replace it (my preference would be to use CPVC pipe for the replacement) and water hammer arrestors would be in order. Water hammer arrestors can be bought or jobsite fabricated. In your case, with the tight space I wold recommend the manufactured ones. Fastening the CPVC to the joists every 2' would be a big help too.
I would replace the vent pipe for the plumbing drains while I was in there. A proper vent is crucial to good drainage and to relieve odors from the line.
Now, about that toilet, It rocks because the floor is uneven or the drain pipe is too high and the toilet is supported only by the drain lne. When you re-do the floor, make sure the closet flange is attached to the floor well (I like to use 4 #14 X 1-1/2" brass wood screws with a phillips head) and use a closed cell foam closet ring rather than a wax ring. If the toilet moves the slightest bit a wax ring will begin to leak; whereas, the foam ring remains resilient and will go along with any rocking. The rocking can be eliminated by cutting small pieces off the PVC pipe at a 1 or 2 degree angle. This makes wedges of the plastic which can be shoved under the bowl to level it up. Then run a bead of silicone caulk around the base of the bowl to seal it and hold the wedges in place. Let us know how it goes and if we can be of further help.