Rejetting shouldn't be necessary until you modify the intake + exhaust, so you're ok there.
Modding the stock exhaust is, as mentioned, not reversible. So if you even *think* you're going to sell the bike in the next 3 years, aftermarket is your better option.
Have you heard a hole-saw bike that you liked, in person? If so, absolutely the route I would recommend. If not, I'd look for & listen to some bikes before cutting anything.
That said, my 750 came with Cobra Street Rods & they are LOUD. They're part of the reason I bought my bike, after riding an equivalent bike with stock exhaust for the same $$$. Installing aftermarket exhaust won't increase your resale value, but may change your customer base.
Replacing & saving your stock exhaust may also allow you to resell your stock exhaust to recoup some of the expense. You won't get $2000 for the stock exhaust, like Honda does, but maybe 1/2 the cost of the V&H or Cobra exhaust.
Food for thought. ...
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