Even with emissions testing, you should be able to get away with a TBI setup. I doubt they would look close enough to see that you are running TBI and not a carb setup, and the TBI will theoretically run cleaner.
In an emissions testing area, if you try to sneak the TBI by them, you would still have to maintain all the other smog stuff, or be faced with possibly failing the visual inspection. If you go with a kit like the Howell, it comes with a sticker that says it is CARB (California Air Resources Board) legal, which would allow you to remove just about all the emissions equipment. This is important if you do something like a full 4.0 engine swap, or even a 4.0 head swap, as I think it would be difficult to retrofit the emissions equipment to a 4.0 engine or head. And that's where you get the real power improvements.
If you do a DIY TBI installation, you can probably still do away with most of the emissions equipment, but to be on the safe side you would need to get it inspected and approved by the Man, and I'm not sure how up to speed they are on a swap like this.
All this being said, sometimes you can go for your emissions test, the kid at the station doesn't know what the heck to look for under the hood, and as long as you pass on the numbers, you have a cat, and your gas cap passes, you're good to go!
They do also look for an O2 sensor, air injection system, and EGR valve. But all of the components can be left on when switching to TBI. So to anyone looking under the hood, unless they know exactly what a carter bbd carb looks like (in which case they probably don't care about enhancing modifications), they won't know that you are running TBI and not a carb.
The O2 sensor is needed for the TBI system, and the AIR system is good for maintaining the catalytic converter. I don't know how many cars used an EGR valve with a TBI setup, but it shouldn't hurt anything.
I've taken my eagle through with a motorcraft carb and open element filter, and they didn't have any problem with it. They just looked for the key components.