CEL Codes
 

I currently have a built engine in my stang, running the stock tune, for the moment. The computer is throwing a CEL (Big surprise [/sarcasm]) and I have a question about them.

P0401 (Insufficient EGR Flow) I have the EGR deleted so no big surprise there

P1000 OBD II Monitor Testing incomplete
This is the one I really don't know anything about, the car wasn't running, and I assume it's throwing this code because of that. But I'm unsure

P1260 Theft Detected Engine Disabled
???? Like I said they car wasn't running, I was using the proper key with the chip and it starts up just fine with that key, it won't start if I use my spare door only key I made at a hardware store to keep in my wallet in case I lock my keys in the car. I've used this to crank the engine over to prime the oil system on the initial start up, and a few times to unflood the engine after disconnecting the battery for one reason or another.

I don't think these are anything to worry about, but I wanted some input before I just ignore these. I know the EGR code will go away when I deactivate it with my tune I should be getting in a few weeks, but like I said, I was unsure about the other two.

P1000 OBD II Monitor Testing incomplete
I had this one Once and It was gone the next time I started my car. It came up after I tuned it and had not started it yet. I think its just a phantom code that comes up before it does its self testing of all the sensors.

neither one of the codes are anything to worry about the P1000 just means that the obd readiness hasnt been checked and the P1260 is because you cranked it over with a non-coded key no big deal.