I wouldn't risk touching the headers, unless you have a personal friend that works at a smog shop and can "overlook" them. By the letter of the law /any/ modification to the exhaust system is illegal and can cause your car to fail smog unless there is a specific exemption sited by CARB or if the part is certified CARB Legal. AFAIK
JBA headers are the only CARB legal headers available for the Thunderbird. But due to their cracking issues, I can't suggest them. That leaves your only option to extrude hone your stock manifolds or find a friend in the SMOG industry.
I removed my intake silencer and I've been smogged with it off. I passed. Unless the guy gets really nosey, lifts your filter and takes exception to the fact that there's an open hole in your fender, you're okay. IOW, unless the guy is a total prick that likes to go beyond the law, you're fine.
As far as the MAF is concerned, I don't know. What I have heard is that an aftermarket chip will cause the computer to throw a code. And since a chip is required to run a different MAF, you'll be throwing a code at the time of the smog test and I believe that's an automatic failure, but I'm not sure. I'm not sure if this is the case should the chip have a factory position setting. Also, a MAF is kinda hard to look at and say, "Ah-hah! This doesn't belong here!" So unless there's a code pointing to the MAF, or the guy starts cross-referencing part numbers..you'll be okay. I'm almost tempted to ask for people to give some input on "good" Smog Places in California.. yanno.. the lazy kind. Make it a sticky of some sort