Emission Test "NOT READY"--O2, EGR, & thermostat sensors will not reset -- NO CHECK ENGINE LIGHT!

When the key is turned, the check engine light does go on. Also, all 3 codes should be clear. The EGR valve, thermostat, and O2 sensor on the exhaust were all replaced. The car was also driven almost 650 miles and completed two drive cycles that should have reset the computer.
The only other possibility is that the PCM itself is faulty, right?

UPDATE! 9 months later, I finally got an SES light. I was planning to get the car checked in April anyhow to give myself plenty of time to diagnose the car further.

On April 12, the car threw 3 codes: P0113, P0404, & P0405. P0113 was the intake air temp. Sensor and the others are EGR codes. The garage I took it to was the same one that worked on it last year. Since two of the 3 codes were the same, they reset the codes and told me to drive it for 2 weeks to see if they came back on. Meanwhile, I looked up an EGR on Amazon as well as a code reader just in case. There was no way I was going to pay over $200 for another EGR after only one year.

Well, the SES light came back on the next day. So, I took it to another garage and got only 2 codes this time: P0404 & P0405. Although both of those codes are EGR codes, the garage recommended that I replace the spark plugs and cables as well. Since I had not done that since I purchased the car, I allowed it. After that, the SES light went out. So, they held off on replacing the EGR and said to drive it and see if the SES stays off.
However, it came back on as soon as I pulled out of the parking lot.

So, I decided to take matters into my own hands. I went on Amazon and purchased a new EGR for $80 and a code reader for $90. Totally worth the investment! I replaced the EGR and reset the codes with my reader--haven't gotten a code in the past 3 days. I'm just running drive cycles to reset all of the monitors and have my next emissions test on 4/29.

I also have plans to replace my car battery after that appointment, pass or fail, because my code reader did a battery test and the battery voltage is reading below the minimum acceptable limit.

I will post an update as it becomes available.

5/4/16:
All of the readiness monitors were green as of 5/1/16. Crossing my fingers that my follow-up emissions test on 5/6/16 comes back passed. If not, PA DMV better have a good reason considering everything about the car shows green.

5/6/16: Car passed emissions. Apparently, all of the readiness monitors have to read green.