I don't want to be a 'bearer of bad tidings' but, If you change the stock exhaust system to an aftermarket system, I'd be putting the stock system away somewhere for probable use in the future.
'Probable' can be soon or not so soon depending on big brother and whether the current spate of legislation gains momentum. Various communities are adopting noise and emissions regulations that could spell and end to aftermarket systems. A good example is Denver where your exhaust system not only has to pass a noise test but has to be 'Agency' stamped and certified and that means if you have a cat box and it's not there, you don't get your plates. The AMA as well as other groups are fighting the legislation but with the current 'Global Warming' trend (I personally think it's all bull****), the movement is on for motorcycle certification. To that end, I'd keep the stock system if you replace it with anything at least for the next owner if you sell the bike. OEM exhaust systems are prohibitively expensive to replace and a non-stock system could cause your re-sale value to plummet rapidly.
I'm 'up the creek' with my Bonnie. I used the stock headers as a jig to replecate a custom system and the mufflers themselves got given away. Oh well, it's a show bike anyway.