Rough idle problem and can't find solution

I have a 96 Ford Ranger 2.3l 5 speed that has been having a rough idle problem for the past 2 or 3 weeks. My truck was running fine and then I had the CEL come on and the code was P0401 or EGR Flow is insufficient. I proceeded to change the EGR Valve and when I did this and started up my truck it was idling rough, so I put the old EGR back on and it didn't fix the rough idle problem. Since then I have changed the EGR Valve, EGR Vacuum Solenoid, EGR Sensor, IAC Valve, Air Filter, Fuel Filter, Upper Oxygen Sensor, Spark Plugs and Wires, and I have cleaned the MAF Sensor and the Intake Manifold and Throttle Body. When I took off the Intake Manifold the hole that goes to the EGR valve was completely clogged and since I cleaned it the CEL has not come back on. I have also had 2 instances of the CEL coming on and it being a Cylinder #2 misfire. Ever since I cleaned the Intake Manifold a week ago I have not had any CEL's. My truck is still idling rough. I took it to Ford and had them do a diagnostic on it and they told me that it wasn't misfiring and that it didn't have any codes stored in the computer. They also did a compression test, which said that cylinder #1 had a low compression by 1% and that cylinder #4 had low compression by 4%. They sent me on my way after telling me that it might be a slightly stretched timing belt and that they would charge $600 to replace it. What a joke! I am at a loss as to what might be the problem. I don't know how to check for vacuum leaks, but that may be the problem. The only other thing I can think of are the fuel injectors, which I don't know how to test. My truck's temperature gauge is also slowing going up and down between 1/4 and 1/2 when it is idling.

I have changed the DPFE otherwise known as EGR Sensor and I have changed the Idle air control and I have cleaned the throttle body.

My P0401 code is gone. It was a plugged up intake manifold port going to the EGR valve.


Thanks for your help!