I had trouble with everything! Kidding... sorta. Michigan doesn't have any emission testing at this time. The only trouble I had was an O2 circuit (I run all four) problem which I fixed, and EVAP stuff which I am still working through. I am running single exhaust and a single cat so I am trying to figure out a way to program out one of the downstream O2 sensors and have the computer look for info from one. It stands to reason I will get slightly better fuel managment with one downstream O2 sensor making corrections. The EVAP stuff I don't think will be real bad I just haven't gotten around to it yet. Lots of info over here http://www.ls1tech.com/forums/conversions-hybrids-28/ A lot of 5.3L stuff comes up in there.
Have you tried wiring up the o2 circuit so that both receive input from the same sensor?
If im not mistaken the o2 sensor spits out a different voltage depending on the fuel/air mixture. So maybe you could just splice some wires together and hopefully it wouldn't change the voltage received by the engines computer.
Or you could always remove the CEL bulb :confused1