I've been having some trouble getting rid of the codes mentioned for about 6 months, but I first got the codes after installing a short ram air intake, the Magnetti Marelli ECU, and an oil catch can around March of last year. The codes had originally popped up a little bit after all three mods had been installed, but they were able to be cleared and the car drove okay without any major issues. August comes around and so the car needs a smog check, but fails the inspection because of readiness monitors that weren't set, and the 4 permanent codes stored in the computer. I've seen the other posts about doing drive cycles to set the monitors and clear the codes, and I've probably done 40 to 50 drive cycles of about 15-20 miles each after removing all three parts, but it just hasn't happened yet and its about to be the car's 9th month not being registered. I've taken it to the dealer to have them check it out and they told me the same things that I've been doing and reading about on the forums.
Something that I notice happen often is when I'm done driving and turn my car off, all the electrics in the car seem to turn off too, so no lights or anything come on when I take my key out of the ignition, and if I had the radio on, it shuts off, and a sound from inside the dash that sounds like a CD changer going off can be heard. I had the battery tested and it turned out to be bad, so it was replaced, and nothing like this had been happening for a while until this week it started back up again. My thinking is that the alternator is bad and is not charging the battery enough when the car is on, so when I go to turn it off it is literally cutting off all power and clearing all the memory in the computer and erasing any progress I could have maybe made in clearing the codes. Thoughts?