Car won't start/run Help PLEASE!

Hello. I have a 1998 Ford Escort Sport 2.0. Recently I broke down and the car would not start. My first instinct was a fuel pump since I have 150,000 miles on the car. I went ahead and replaced the fuel pump. After further inspection I determined I had no compression in 2 cylinders. After tearing into the motor I determined that a valve seat went loose and tore apart the motor. I went ahead and replaced the entire motor with 60,000 mile junk yard motor. New motor has great compression. I put about 500 miles on this new motor when I broke down again. This time I was doing 60 mph and all of a sudden I lost all power (the motor lost all power, all of the lights still worked and the horn) and I pulled over and the engine died. Now I checked all of the obvious. I have 13 volts at the battery, and I had the alternator checked and it was good. I replaced the fuel filter (I don't have a pressure checker but since I just replaced the fuel pump I feel I am good here.) I have spark in all 4 plugs. I plugged in my CanOBD2 emissions code reader and it came up clear. I checked all of the cylinders for compression again and they are all good. Since I have fuel, spark and compression, I figured it should run. I went to go start the car, and it fired up but it would not want to idle. I had it running for about 30 seconds and the rpm's were above 2,000. Once I left off the gas, it died. Now it will not start at all. Can someone please give me some further ideas to try? Has anyone else had this problem? Please help!