On occasion it won't start?

My daughters mustang standard edition. She has poured the money into this money pit as well as I have. She put a motor out of a junk yard in it and it runs like a champ but on occasion it won't start. It acts as if it's loading up sometimes and you have to blow it out. Sometimes during driving it will do the same thing usually while she is at rest at a stop light. We have replace the Mass air flow sensor, the fuel pump and filter twice, had the fuel pressure checked. Vacuum checked for leaks. Fuel injector removed and cleaned. Run at least a gallon of Lucas and only use premium gas. Can you help me out please.