Sounds like dirty fuel, my advice even thou it's running fine now, empty the tank flush it out so there's no particals in there, change all fuel filters, next time you run the engine run a jet/injector cleaner thru it (mixed in 5litres should be fine and run till near empty) then change filters again and you would be good to go. If you have a built in tank you should install a water seperator. It'll be the best investment you'll make engine wise.