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how long have you tried to start it after doing the repair?
it sounds like one of the pushrods has jumped out of place, if it is popping out the intake then it is an exhaust one, if the system was apart, it will build pressure and fire, then it grabs a big gulp of air from the system and you have to crank it back up until the high pressure pump reservoir fills up again. I would first remove the valve covers and check all the pushrods
do you need more help?