If it is the first time you have driven it since the engine swap, you will of had battery unplugged for a while. This im told on my98 car resets ECU, it looses everything, mine used to stall at junctions, jerk about, run rough as toast. It only happened everytime i unplugged battery for a while (say over an hour). My neighbour told me (a mechanic) that the ECU has to learn your driving style again, throttle position etc. this maybe whats wrong with it mate. If so good 50mile trip will sort it out.