Most of the time when one cylinder runs and one doesn't, the problem is dirty carbs.
www.amckayltd.com/carbguide.pdf is the best source of info on our carbs. Read it, print it out and read it. Read it till it starts to make sense.
Now put it too use by following the steps to tear down, clean, inspect what you have. Pay particular attention to the idle and enrichener circuits.
Now if your inspection reveals worn or damaged parts buy just the parts you need.
These carbs, with some varaition where used on many bikes other than the XS650. Most carb kits may work with the most popular bikes but seldom work well on ours. The float bowl gasket and float valve are about all that work.
When you do the tear down and cleaning. write down all the numbers on the brass parts.
There is a chart on what these brass parts are by year of the carbs in the carb guide. Compare what you have against what the chart says should be in there.
A PO may have been in there and bot the wreong parts inthere.
Leo