It's probably also worth pointing out that emissions equipment (and therefore ECU programming) can differ based on whether a vehicle is manual or automatic, and this is nothing new - this goes back to the late sixties with american stuff at least.
I have never seen a vehicles emissions differ based on what tranny it came with. I have seen slight tweaks of the fuel mapping based on tranny choice (auto's can have a slightly more agressive fuel curve to deal with the power consumption of the auto) But never a difference in actual emissions equipment.
Please dig up the rules, I would love to know if there is somethign I am missing.
Again, there are multiple manual transmissions and automatic transmissions that can be configured with a certain motor from the factory. That does not mean that you have to install the exact same transmission that a car originally came with. It means that the combo had to be available somewhere. Do some research, Vettes still come with manual trannies as do pickup trucks. I have also never seen the inspectors ask to see the actual computer that you are running to verify what tranny it was designed for. If it throws codes, then you have an issue, but as was said, a lot of the computers now a days are essentially open code that can be reprogrammed to do what you need. The engine swap is based on the casting number on the block. Not the heads, cam, valves or anything else. As long as the necessary emissions are there and it passes smog, you are good.
EPA has certified alterations in cats. Running one instead of three for example.
The EPA has also taken to adopting Californias standards as much of a PITA as that is. And honestly, it is not that big of a deal.
1st at 60 mph would be screamin.. My 60 with a C6 and 35" tires does 80 ish at 5K in second.
A direct drive with 4.10 gearing, 35" tires and a 2.48 ratio in the transmission is pushing 5900 rpm