I went through all the same research on this about a year ago. Here is the summary of what I found out: You are correct on most of the basics.
1) On a '99 ULEV Accord, you have to use a '99 or newer USDM Prelude engine. The CARB regulations say that "A California certified car must use a California certified engine." The ULEV is a California certified car, which means that the Prelude engine must either be from a USDM Prelude, or you might get away with a JDM engine if the engine is an exact replacement for the USDM engine, and you would still need whatever USDM smog pieces the JDM engine did not come with.
2) Once you complete the swap, you make an appointment with a Referee station. The phone number is available on the California Air Resources Board website. Most referee stations are located at junior colleges, and the referee is usually the autoshop professor. You can actually contact the referee ahead of time and talk to him about your swap if you want to.
3) If the referee has not seen your swap before, he is going to go to the computer to look up what it ought to have, and this means he probably will look at your ECU. If you use any ECU other than what came with the engine, you can count on an automatic fail.
4) You have to use the transmission that came with the engine you are swapping in. When you buy your engine, make sure a manual tranny comes with it, and do the whole swap/conversion at the same time. You might get away with fudging on this one, as long as the trans you are using is one that could have come with the Prelude engine.
5) Best way to "get over" with the referee is to use all of your parts from the same donor car, and have title docs available for the car, to prove origin of the engine and all the other parts. I learned this from a guy who swapped a Ford V8 into a Mazda RX-7 -- and passed ref.
6) Some referees are laid back, and some are real @$$wholes. I've seen CRX guys with JDM B16's pass referee and get their sticker, and I've seen some BMW guys who swapped later M3 engines into their 318's or 320's just get hosed for not hooking up the charcoal canister for the fuel vapor recovery system. Talk to the ref ahead of time, and if you don't like the way it feels, find another ref.
7) It is probably best to leave the engine stock, right down to the airbox, when you finish the swap and take it to the ref. The fewer excuses he has to fail your car, the better.
8) When all is said and done, you should get from the ref a little sticker that goes on the driver's doorjamb, which identifies the car, and the type of new engine. This sticker gives you the "magic immunity" when the police ask you to lift your hood.
This is the sum of more than a year of internet research and gumshoe work. I have spoken with a couple of referees, and these guys are just like anyone else in a position of authority. They have rules to follow, and they get in trouble for breaking those rules. Do things right, make it easy for them to follow their rules, and you'll get that sticker.
Chas
