2003 Kia Spectra Engine swapped

I am working on a 2003 Spectra 1.8L and the owner wanted it swapped with 2004 Spectra 1.8L engine. The new engine is installed and it starts but, when idleing at 3300 rpm's the motor surges to 4000rpm's and shakes before it rev's up. I changed the fuel rail and injectors, tb and both sensors, checked all wiring, changed out the plugs (new but fouled out on start up), and now I am stuck.
The engine was sitting in a junk yard for a few years which is why I changed many items.

Please Help

Eric (Detroit, MI (suburb))