Engine gerks going down the road,cuts off some time when recranking the car back up?

my1999 olds alero v6 engine started gerking and lost power so i replaced the engine with a 2003 used engine with low miles, and its skipping to. and when i cut the car off some times say to get gas and try to restart the car it will cut off. i haft to restart it several times and give it gas to keep it running then its fine, and will keep runing. ive replaced spark plugs.wires,fuel filter ,and my mecanic has reset the COMPUTER , disconnected the BATTERY for a few mins. then reset the COMPUTER by rebing up the engine 5 time to the reb limitor ,but car doesent show any bad codes .my mecanic doesn't no what is causeing the problem hes asked me if i can live with it .im warried it may do damage to the engine down the road .if theres any one that can help me please let me no . im wondering could it be the fly wheel are tork convertor ,or fuel pump?my gas Gage stoped working a while back and i plan on replacing it soon. i don't wont to mess up this engine ive sunk a lot of money in to my car .help me if you can.!!!!!!!