Yamaha 535 stalling out and losing power after running for a bit

Make sure the fuel system is properly vented (gas cap, carburetors) Make sure the petcock will freely flow fuel, If this is a vacuum system, make sure you do not have any vacuum leaks!! The carbs sound like they need a good professional clearing, setting, and synchronizing!!

Only running good with the choke on is an indicator that the bike is normally running too lean. The fact that it runs good with the choke on at least tells me it is getting fuel to the carb(s). Therefore it seems probable that there is clogging in the carburetor jets or there is a big air leak between the engine and carb(s).

You seem to have missed the air filter.

Yamaha motorcycles of this vintage often have issues with their kickstand switch. This switch can be disabled by clipping the two wires that go into the switch and wiring them together--the kickstand switch is normally closed (letting current flow) when the stand is up; the switch is open when the kickstand is down.
This is more afield than your electrical concerns, but if the clutch plates have bonded together, the bike will stall when you put the bike into gear. The bike will start and idle fine, but basically, you don't have a working clutch, so the bike will stall out when you dump it into gear while at a standstill. You can test for this by starting the bike and having someone push the bike to get up to a little speed, then trying to shift into 2nd gear. If the bike lurches forward before stalling or keeps running, you have a clutch, not an electrical issue.
Folks sometimes get lucky, and working the clutch plates a few times will free up the sticking plates. I have had this problem with a mid-1970s vintage Honda that I don't ride very often. Eventually, the clutch plates free up and the bike is good to ride again.
Good luck!

hi,generally speaking yes,they have a very forgiving engine with gentle power delivery(no sudden surges of power like sports bikes)they are also very comfy to ride and yet even though it is only a 250 it will cruise quite comfortably at highway speed..enjoy..hope this helps

You may have a fuel problem ,try cleaning out your main jets and try running with no air cleaner .it may need changing ,and a new one fitted

check your idle speed.you should have about 1 cm of free play in the lever.also does it start up agian and are you able to drive it if not check your side stand switch

fuel filters are in the carbs!
[very fine wire mesh] throw them away & put inline filters on the fuel lines!!!!!!
Cheers Rob

Check for vacume leaks first. Rubber lines..gaskets to carbs ect. Also remove and blow out your fuel line to tank and change out filter. Hope this helps.:)

Sounds like it is starving for fuel. change the fuel filter. May have trash clogging it up. If problem still continues check your plugs for spark when it dies and wont crank. This would lead to bad coil or ignition module.