Are there any other modifications? Intake, Bore, Stroke, carburetion?
There is tuning, but to really take any advantage of it, you need to have the engine on a dyno. Small differences, if you are looking for the absolute max, can make significant differences.
For instance, is the inside wall have a higher or lower mach number then the surface of the stock?
Twice the are is half the velocity. Too low a velocity made reduce scavenging, and cause a loss in performance. Also, are you tuning to high RPM, Low RPM, mid range? The intake and exhaust are generally tuned to a small, specific range of RPM. Racers keep the engine in that range as much as possible.
For street riding, usually the low to midrange RPM tuning gives the best response.
So yes, tuning the exhaust is important. The stock exhaust were usually tuned for street, fairly wide range of torque, emphasis on the bottom end where most street riding is done.
You can tune for peak HP, but have a nearly un-ridable for the street tune.
Duplicating the stock exhaust in size and length will probably give you the best driveability.
Since you appear to be going larger, you need to follow some general rules of thumb...but you need to have a goal for it.
If you ask me, and you did ask for opinions, the greater performance would come in the reduction of weight a custom exhaust would have. If you duplicate the stock path, size and length but reduce the weight by 10-12 pounds, that would actually be a noticeable increase in motorcycle performance.
Shortening the exhaust, increasing pipe size significantly, may improve some places, lower others.