I had my bike jetted once but it never ran right at all to my liking so i had it put back to standard, and it ran fine with any exhaust after that.
Unless you're going full on, like using carb pods, then they don't need jetting, but as suggested if it has been altered then it could make a big difference if the original exhaust is put back on.
I changed my stock exhaust straight away because i didn't like the look or sound of it, but the bloke who used to Dyno my bike said the stock exhaust headers are better than any aftermarket ones, it was just the build quality that let them down.
You don't actually mention if your headers are stock or not? And when you say original exhaust do you mean the headers or the end can?
Again as mentioned a carb balance could no doubt help, but also check for any leaks around the gasket area as they can be fiddly and if there is any escaping air then it will markedly affect performance.
Something else to bear in mind is the condition of your air filter as well. Any, or even all of these things can make a big difference in running.