Did you restore wiring back to 100% stock? Removed all extra wiring, crimps and tape? Sealed up any exposed wiring with heat-shrink wrap? You might have short somewhere.
First, use this procedure to have it blink error-codes:
https://faq.ninja250.org/wiki/Fuel_i...des_for_EX250K
Will point you in direction for closer inspection.
EFI engines are extremely sensitive to vacuum-leaks and sensor calibrations:
1. Measure vacuum at MAP-sensor at idle with cold engine
2. Measure vacuum at MAP-sensor at idle with warm engine
(Use rubber T so MAP-sensor AND vacuum gauge can be connected at same time)
3. Measure voltage-output of TPS while going from idle to WOT (key ON, engine not running). Look for any sudden jumps in voltage. Should change incrementally and smoothly with no jumps or dropouts
4. Measure idle-switch in TPS. Should be connected when throttle released. Circuit open as soon as you twist throttle
5. Disconnect O2-sensor and drive around. Does it still stall?
6. Measure voltage going into fuel-pump at fuel-pump connector. With bike idling, wiggle wiring harness going to pump, does it lose voltage and die? Do road-test, Tape voltmeter on dash and drive around. If it stalls, what is voltage going to fuel-pump just before and after it stalls?
7. Injectors & connectors. Wiggle wiring going to injectors. Does that cause stalling?