Can't get bike to go past 140km/h, 1979 xs650SE

No, it's not common for the whole charging system to die. It's usually just one of the components. Top of the list are the brushes (wear item) and the rotor going bad. Then sometimes the regulator will crap out, but it's pretty reliable. But, you can replace it with a low cost automotive regulator that is very reliable. I quite like the original charging system. It's a 3 phase automotive type system, well proven and quite reliable. Yes, parts are failing on them now, but they're 40+ years old. I would never switch to a PMA (Pain-inMy-Ass or Piss-Money-Away, take your pick, lol). They cost hundreds of dollars and fail more often than the old original system it seems.
Okay good to know. I'll start digging into the low charging aspect. Most likely brushes/rotor, as a bad regulator would cause a overcharge condition and diodes a no charge condition if I'm correct?
Maybe I'll try a new battery before doing the alternator swap and see what that does. Is it common for the whole charging system to just die or is it just maintenance related like replacing brushes/diodes? Read alot that it's common for the charging system to die but it seems to be a blanket term.
There's a lot of good info on this site on the charging system - not discussed as blanket term, but very specific - as with any electrical it should be checked in a logical manner.

The stock system is very repairable, the PMA's not so much (I've got both).
Not read through it all
But the 1979 here in Europe would have Points and Mechanical regulator.
The mechanical regulator is adjustable. Up and Down ..And can be a way forward .Some say it is good enough.
Saving costs. At least in the short time.
Electronic is better especially if electronic ignition is in the Plan.
A low voltage can affect the spark .But Mr 5T says the plugs look OK.
I always have had more black ones .And not having problems.
But having said that rarely going for +140 Not wanting to trash the engine.
Yeah I forgot to hold the throttle open, was thinking about that on the way home lol. Probably expect around 100psi cold with throttle open.
Not holding the throttle open can reduce compression readings by more than 50 psi. Compression testing a cold engine will usualy reduce readings by only 5 - 10%.
You have to keep in mind that these are only about 50HP bikes. Gear it too high, like much below a 32T on the rear, and it most likely won't even pull 6K in 5th, lol.
A Special with buckhorns, stock mirrors, and a rider in loose clothing is hardly aerodynamic. In addition, the issue here may also be lack of power, gearing, tacho accuracy and speedo accuracy.
If it had 50 ACTUAL rwhp, it should do 180 ACTUAL km/h (112-113 mph). With a prone rider/ low handlebar.
My 95 Ducati Monster 600 dynoed at 53rwhp with basic mods. After that I fitted a 680 kit, hopefully adding a few more hp, maybe up to 56-57. In that state it did 190 kph on a calibrated electronic speedo, with me prone, in fairly tight leathers and only one small bar end mirror.
A somewhat tired 650 Special with 40 or less rwhp and a bolt upright rider would struggle to do 150 kph.
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My SG with a bone stock 10,000-mile engine, from the intake tubes in the airbox to the tips of the pipes, 17-32 gearing, and an 85-mph speedo will just sneak past the 85 (figure 87-88 mph). Buckhorn bars, 2 stock rearview mirrors, and a 6'2", 260lb rider sitting bolt-upright. The engine tests and runs fine, >160psi compression and <2% leakdown, and stock jetting. It's perfect for cruising the backroads at 40-55mph. Approaching redline in 5th is never an issue, it just won't happen. I just finished refurbing a '76 XS, but have yet to test it for top speed, although I do have a 24T 5th gear in the trans, so I suspect that may limit top end. If I want to go fast, I have a Kawasaki ZG1000 Concours that'll do 140mph+ in 5th (It has a 6th gear, but won't pull 6th above 125 or so).