Everything is back together, used the kneadable epoxy and a washer to plug the hole in the muffler. I figured out that the hole was there because that is where the centrestand ended up contacting. After i get a new pair of muffler that aren't made out of italian rust-magnet mild steel (these new ones are made in the USA) i'll have to put a little rubber lug on the muffler /the centrestand to stop it happening again.
Tomorrow i need to get more muffler wrap as i have to cut back/replace some of the wrap that is on the crossover as it's making a god-awful racket. Fingers crossed that aside from the muffler replacement in the near future, this is the end of it all.