Non expert warning: I have NOT rejetted non stock XS's
The canard that less restrictive exhaust must equal bigger jets is tired and untrue. It is not unusual to have to lean the jets to get the best engine operation. The carbs provide an air fuel mixture. In general more air through the carb automatically equals more fuel. If that wasn't true your engine would not be able to accelerate from 5K RPM to 7K RPM under WFO As the engine pulls more air at increased RPM it also pulls more gas. It's the very definition of carburetor. Now that said there is a limit to how much gas can flow through the jet no matter how fast the air flows. So IF your exhaust (and other mods) allow your engine to make more horsepower at some point you will need a bigger jet to get enough fuel through the engine to make that horsepower. Straight pipe open exhaust likely makes noise not power, megaphones and other "extractor" type exhausts that are properly engineered to the engine can need richer jetting. So after all that my advice is...
#1 leave the blasted mufflers ON. Good god the world is plenty loud already.
#2 when you cut them off ( I know, you will) leave the jetting where it is and do chops. Full throttle run, kill the engine, stop and read plugs. Decide THEN whether you are rich or lean go up or down a jet size, repeat.
After three or four or more tests like this the main jets will be close then you have to work on the mid jets and needle jets.
A knowledgeable tuner could probably get it done well in a day or two. A backyarder waiting for parts, a few weeks to months maybe.
This is a very involved, work filled, subtle process that is not easy for a non expert.
#3 buy pipes from someone who has done the work to give you an idea of jetting for them. Then at least you have somewhere to start from.
#4 Drill the pipes weld on adapters and install EGT gauges. That will reduce the time to arrive at correct jetting.
Pipe length is critical, the length of pipe from engine to muffler (or end) will change the power characteristics of the engine. Much of this work on the XS650 has been done for you a little googling will reveal ideal header pipe lengths for different engine power bands.