I have a L2550, I removed the battery and parked it in the barn for about 18 mos. It has 1450 hrs. and it's a late 80's model. I started it and the engine went full throttle, turning off the key and pulling the manual fuel shut off wouldn't stop it. I had to put my hand over the intake tube to choke it to a stop. The linkage for both the hand and foot throttle are functioning normally as is the shut off solenoid. The tractor was operating just fine when I parked it. Is something inside the Injector pump stuck?
Glad you escaped this event unharmed.
Never stick your hand over the intake of a run-a-way engine.
A board, a towel, anything but you.
The sure fire way is to use a CO2 fire extinguisher. It cuts off the air supply.
Many newer Kubota's are being recalled for freezing crankcase vent systems which result in a run-a-way. Pressure builds in the crankcase because the vent system is frozen, The added pressure forces crankcase oil up the turbo drain line and next you have not control over the engine as it has its own fuel supply.
You likely have problems inside the injection pump but there are other reasons for a run-a-way.
Dave