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I assume there are no CEL's?
Since you are running a CA ECU lean burn should not be an issue, and technically the car should pass the emissions test. You mentioned the possibility of a misfire. You would be able to tell if there was a misfire. It shakes the car, doesn't sound or feel right at all. However, it is possible one or more of your cylinders is leaking compression, creating inefficient combustion and therefore higher emissions.
I didn't read through your whole build, so you might have already done this. But rent a compression tester and test each cylinder. If that checks out I would replace your CAT. 2 CATs is not really helping. The CAT is expecting a certain mixture of gases that will react inside, and produce different gases as exhaust. When you are feeding exhaust from one CAT into another, who knows what goes on inside the other one. This topic is interesting because lean burn engines actually emit lower NO2 and CO2 than a normal burn engine out of the exhaust ports. But due to the reaction inside the CAT, which is designed for normal burn exhaust, the emissions from the normal burn engine actually come out cleaner. Lean burn engines need special CATs to handle the different mixture of exhaust gases to efficiently react with them.
The compression test is where I would start, it's free and easy. If indeed compression is low it's plausible that is the cause of your emissions failure.
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