If that was the way it was when the bike was turned over to you and didn't just happen sometime afterward then I am also thinking the kickstart shaft was not fully wound before installing the stop bolt. Just like a person should run through all the gears of the transmission before buttoning up the engine, so should they confirm that the kickstart assembly is as it should be.
While the stop bolt is accessible after removing the clutch cover, I'm pretty sure you would not be able to complete the wind without pressing the ratchet pawl down to clear the ratchet gear (splitting crankcase needed) as I describe below. I'm thinking you would just loose what little you have now.
Return spring broken or its anchor ends out of place?.... Thin wall of pocket for spring end broken out during crankcase assembly?..............
Though the kickstart spring did break several years ago on my T500, unlike what yours is doing, my kickstart lever/shaft would not return at all. If memory serves me correctly, it was the end of the spring that goes through the shaft itself but I can see it happening on either end or even damage
If it comes down to you having to split the cases, go ahead and install a new kickstart pawl, pin and spring. More 'meat' in this pawl/ratchet gear assembly, the better. That way you will know for sure you have brand new one in there.
There are two ways to pre-wind the kickstart shaft....both maybe a little hard to describe. The way I do it just takes seconds after shaft is installed.
(1) Stop bolt out or at least backed out enough to allow the stopper on the gear end of shaft to clear as it comes around.
(2) Install kickstart assembly making sure end caps are lined up with locator dowell pins and ALL THE WAY DOWN....double check. Tighten shaft clamp down.
(3) With lower crankcase on bench, kickstart lever overhanging bench..... wind the kickstart shaft around with the lever....it's going to stop before you finish the full wind. At this point you just press the pawl down with a small screwdriver or pick (you clear the ratchet gear by doing this) and that will allow you to bring the stopper on around and past the stop bolt....hold...now go ahead and run the stop bolt in all the way....you can now release the shaft and TIGHTEN the stop bolt. Re-position the kickstart lever on the shaft splines as needed.
I'm pretty sure I have not missed any steps but it has been a long time since I did it last and I'm old.
On the bad noise coming from a cylinder after somebody just 'rebuilt' the engine.......as you already know, if a hard seize occurred suddenly while riding, that could be very dangerous.
As far as the cause of the noise....... speculation is all I or anyone else could offer at this point.
Damn shame about the problems you are having with your new purchase.
Good Luck

