Luckily, after all the many changes, it started again. But from this point on I would only proceed step by step, otherwise you won't know whether new problems have arisen in addition to the original one and what they are.
The fact is that it was running when you bought it. So there can't be so much broken that would require replacing half the engine as a precaution.
I'm writing this because the exact same thing happened to me: At the location of sale the XS started but produced a few misfires here and there. Back home, after 150 miles on the trailer she no longer showed any sign of life. Electric starter, kicker, all to no avail. The battery had full voltage. The plugs produced sparks in the open air, but were completely black and wet.
Well, everything looked like I had a major carb problem, or at least that it was running way too rich. But in reality, the ignition timing turned out to be completely wrong on both sides, and this much too early. The contact ignition on the XS seems to tend in this direction without frequent maintenance, at least this wasn't my first case of this kind.
Anyway, after setting it up correctly, she still didn't say anything. When examining the spark plugs more closely, i noticed that some of the sparks were hitting ground directly sideways from the anode insulation. The problem with NGK's is often that the insulator fails once it has been completely soaked in gasoline. Sometimes the function can be restored by strong heating, sometimes not.
However, with new NGK's, this XS runs perfectly once the ignition was set correctly and usually starts straight away on the first kick. The spark plugs are nice and light brown. Other than adjusting the ignition and replacing the plugs, I hadn't done anything up to that point.
So in this case it was a small cause with big effect, but with hints into the wrong direction and with similar symptoms to your bike. The fact that yours started again with new plugs also indicates this. Of course, if the cause is not eliminated, they will soon fail again. But it definitely makes sense to check the simplest things first before you start replacing parts everywhere at the same time.
And another piece of advice that has already been given: if in doubt, only give the bike to someone who is familiar with the XS. Decades of experience with a particular vehicle are priceless and can't be caught up on so quickly