I'd remove the entire exhaust system as an assembly and replace it with reproduction parts. When an original wear item is that worn out it really doesn't make much sense to leave it on the car to wear further and in most peoples opinion replacing it will not take the car out of "Survivor" status either, just as long as you hang onto the original parts.

So, by all means, if you do swap it out keep the original stuff and hang it in the rafters or some other easy to access area near the car. Nuts bolts, clamps etc. should stay with it as well neatly marked and bagged, maybe even toss in a CD with lots of pics before removal for future reference value.