Is the fuel shut off lever pushed all the way in? If you follow the shut off cable you will see it goes into the pump at a cover that is held onwith two screws. Take that cover off and stick your finger in there and physically push the shut off toward the front of the engine. Sometimes they stick. OR, sometimes when a Bosch type injector fails, it lets compression into the system through the nozzle. If when you replaced the broken/missing bolts you didn't tighten them evenly..IIRC they only torque to around 20 ft lbs... it could put the nozzle in a bind causing the pintle to stick open. This will let compression back up through the nozzle 'cause the pintle is now un seated. Try loosening the injector hold down and re tightening it evenly