An unusual situation, normally the stock pilot jet is fine unless you have a heavily modded motor.
Couple of questions.
Is the pilot circuit scrupiously clean? Even minute dirt in there will cause problems.
Is the boot sealing to the carby?
Could the carby cap be leaking in air?
Is the oil injection nipple on the carby blocked off?
Is the brass washer under the main jet?
Could the throttle cable be tight, kinked or frayed?
When you did the leak down test did you flex the rubber boot, as I have known them to have small cracks which only show their ugly heads under vibration?
Some good info there would of never thought of this!!!