So I read one of the documents in the passkey thread and tried the how it said to program the system if you had replaced the PCM or BCM.
So what I did was put the key in the ignition turn it to on and try and start it. Then leave the key in the on position for 10 minutes.
The thing I read said to do it 3 times and it would make the PCM and the BCM talk and check that they have the same info.
Well after waiting 10 minutes and then turning the car off and waiting a minute the car started right up.
I let it run for about 10 minutes and then turned it off and used the spare key and it started back up again.
Going to have some dinner and try it again, and then again in the morning.
But it looks like I got it working.