Myself and others have done pretty intersting things in California and lived to tell.
First, a friend is running a 3.1L with 1.6 rockers, Blue Racer cam, 8.5 pistons, heads milled .060" (my god!). He passes fine. EGR must work. He is using the 85 1226869 ECM and a Stage II H***rt**h chip (the one with all of the changes only at sub-freezing sections of the tables). He was *dyno'd* and blew well below the limits. He has an MSD also. I don't think this had much affect.
In you case, you are trying pass off the 3.1L as a 2.8L. Say nothing and nothing will be found. Of course if the cat is bad and the EGR is failing and the plugs are worn and the valve guides are shot and the PCV is plugged, well good luck.
On swaps, it is actually about as easy. BAR (not CARB), basically just wants you to do a complete swap and do it right. If you get bitchy with them, they will beat you about the head and shoulder with a large stick. If you go in honest and clean, they are very good. Of course it depends on the referee, but they are actually thrilled to check out a swap. Of course they place secrets on your first try, but once they know you did your research, they are pretty good. Off you go with your bar sticker.
This includes the managemet of BAR. I swapped a 92 3800 SC into my 1986 Ciera. I called and gave them the story. "Do I need a BAR sticker?" On two seperate calls, the answer was "No, not really since you are just using a newer engine. You might want to consider it if you get any grief from a test station". If the emissions list matches, many stations will do it. Now if they think you are a "plant" (undercover), they will reject it.
The point is, 1) the 3.1L bulit correctly will pass the dyno (use a new cat!). Second, swaps are almost encouraged. How can they complain about us putting a cleaner and newer engine in an older car? They don't. Just do it right. If it uses a single cat, use a single cat. CCP? Use the CCP. Use the stock air cleaner.
Terry