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What is the code? If its saying the y isn't changing its trying to tell you the cat is not functioning. Does it still have CATS? You mention it had mods from before, if there are no CATS you need to disable the code in the tune. Tough to say for sure without looking at it. Could be a few things.
Are you running hi flow cats? How are you reading the O2 sensors? You would have to be reading both a front sensor and a rear sensor at the same time to know they are reading the same. That sounds like a lot of trouble when all you have to do is turn off the rear sensors with some sort of tuning software or handheld.