Not sure on the vibrations, but you need a chip and CO setup. I wouldn't recommend riding it too long without this.
Silicone should be good. Although it works fine don't use 'gun gum' exhaust cement because, you'll be cursing when you want to remove the pipes. As for running it with the original ECU, firstly find out what ECU it has? if not suitable I'm sure you can get one from CJS/Louigimoto or JHP and then get it setup properly, but the best solution would be to get it custom mapped by CJS CJS RACING Ducati Cylinder Heads Tuning Gas Flow Dyno ECU Custom Mapping Bristol Bath .