Probe running rough

I just bought a 97 Probe. And got screwed. I have replaced the engine, clutch, timing belt, and the transmission tomorrow. My car idles rough and acts like it wants to cut off. I know that when the people installed my engine they did not connect the EGR valve, but i've heard your car and run without it. When i had it checked only the tranny code came up. Do i need to have it connected or might it be something else? Or do i just need to get rid of this car?

any loose vaccuum hose causing leaks or maybe cracks or leaks in the intake after the MAF sensor can ruin a good idle. maybe a bad TPS or dirty throttle body.