I'm going out on a limb, since my experience with Honda as a tech is almost non-existent. There is a similar problem with the V6 Audi A4's and A6's which I DO work on. The car won't start sometimes, and it's flooded, so I have to step on the gas for a couple minutes while cranking before it fires up, and then there is a huge amount of black smoke out of the tailpipe. The problem there, is the sensor which measures the coolant temperature. The CEL doesn't come on either, but if I check a different control unit for faults, there will be a fault for the coolant temp sensor. The sensor tells the ECM that the engine is extremely cold, so it dumps fuel into it.

Now, getting to the point...if your problem IS a emission control problem..I don't see where your audio equipment had anything to do with it. So take your car to a dealer or your favorite local mechanic, and find out what the problem actually IS, before you go blaming your audio equipment. Sh*t happens at the most wierdest time, sometimes.