Did it do this before you replaced the engine? It is less likely a wire than a bad connection or a bad sensor. Also make sure that it is the correct throttle body for the engine; swap out the old one if you have it and see what happens. A chugging or jerking at certain light throttle conditions usually mean a improper mixture (I think too lean is more likely). Check for codes if you haven't already; that may give you a clue (or lead you wildly astray). No-starts are easy to fix compared to not running quite right, I've found.