Lots of people think the XS650 clutch lever is hard to pull. Most are wrong, they are used to more modern bikes that don't have the clutch cable hooked to anything. Well at least that's how some new bikes feel to me.
As Airwolfe mentioned a well lubed cable and actuator mechanism makes the lever pull easier.
In your repair manual they list two ways to lube a cable, the spray can lube stuff is a poor choice. Use the oil method. Remove the cable, hang it up. make a kitchen foil funnel on the top, fill with oil. Let set, when oil drips out, it's lubed.
Using one of those clamp on cable luber things works ok for cleaning the cable. I use a cleaner with a straw and spray that through the cable. It way take a few tries but spray, pull the cable in/out of the housing, spray, repeat as needed till clean stuff comes out.
Then let dry and do the oil method.
Oil lubes better and lasts much longer than any spray lube.
On thr poor running it's most ;likely the carbs.
www.amckayltd/com/carbguide.pdf will help with that.
On the smoking, if it has set very long the rings, cylinders get a thin coat of rust that prevents a good ring to cylinder seal. Often the best fix is just ride it. As the eng9ine runs it will wear away this rust and then seal up. Stopping the smoking.
By "magnetic charging system" I assume you mean a PMA. Even the stock system is a magnetic charging system. A charging system can't function with out a magnet. The stock system uses an electromagnet. The PMA uses a permanent magnet.
I might not be so quick to do the swap. The stock system works very well.
It just needs a good battery to keep working well. That's the only advantage the PMA has. It can be run without a battery. Anything else is just hype.
Yes, get at least the downloadable repair manual. I have the Clymer, the Haynes and the factory manuals for all years. I use them all.
I like real books. Most of what I have are real books but some are downloads.
When you get a manual do a tune up. Do the steps in order,
Cam chain tension,
Valve adjustment,
If points, points gap and timing, If TCI then just timing check.
Once you get this done along with a carb tear down and cleaning, the bike should run well.
On the carb cleaning, DON'T buy carb kits. Most don't have the right parts. The stock gaskets are pretty robust and if careful can be reused.
Follow the steps in the carb guide to tear down the carbs, inspect all the parts. If any are found to be bad then buy just the parts you need.
Often a float bowl gasket is all you need. Around $5. A carb kit is around $22.
Leo