I got the relearn procedure to work yesterday. Here is what I did different then the instructions mentioned above. Hopefully, other people don't have the same problem.
First off, the clutch does not need to be pushed in for the 6mt.
I disconnected the battery for about 10 hours. The Accelerator Pedal Release Position Learning and the Throttle Valve Closed Position Learning are self explanatory.
For the Idle Air Volume Learning, I started the engine and drove around for 15 minutes. Before, I was just warming up the engine and heard from other people that this does not work.
Then, I followed the step until #5 of the instructions above. Before, I pressed and released the pedal 5 times within 5 secs and afterwards waited 7 secs and proceeded to the next step. Yesterday, I waited the full 5 seconds and waited another 7 secs.
Then, I pressed the pedal for 20 secs. After 20 secs, the CEL stopped blinking and was on. I released the pedal and turned the engine on within 3 secs and it started to idle like normal. I drove the car today and it seems like the ECM didn't forget what it learned.