MustangBoy5.0

i bought a 95 mustang 5.0 for $2,000 with a blown motor so i just swaped in a another 5.0 motor with 54k miles on it from a cougar,now it cranks up runs find idles fine revs fine...but now the weird problem is i crank it up in the morning hit the gas and it lags.. all you hear is the engine basically revving with a little pull...the damn car runs like a v6 all day,some times i hit the gas and it puts you back in your seat like a true v8 but at the same time the engine knocks like something advanceing the timingithas the true v8 power like ounce a day for about 10 seconds only then go away wtf?...when i hit the gas it wants to run like a v8and after about 5k on the rpm the rpm needle bounces and the car lags power... the check engine lght comes on some time,i changed the fuel filter,air filter checked the engine codes 311 and code 314 any ideas before i take it to a mechanic shop and pay $100 to run a diagnostic wich doesnt guarantee to find the problem?