If it's the "insufficient EGR flow" that's being set, there are a couple of members who've done the turbo back exhaust. One kept getting the error code until he put the stock exhaust back on it. Another member with a different brand of exhaust system has not had any problems with his setting codes.
The LLY computers will monitor EGR flow, whether or not there is a way to disable or correct that reading for lower flows due to less exhaust back pressure is something I'm not qualified to speak to, but I've not seen anything here about programmers that will do that. There has been some disscussion about this type of problem on the 6.0 PSD's, but it's just starting to show up on the LLY's since they're still relatively new.
Maybe some other members will have more information for you, but as far as I know, no one's been able to pin down a fix for it yet. Some trucks do it, and some don't...
One of the members put his whole system back on to resolve the problem.
One of the members has an LLY with an ATS turbo back system and has not had a problem with it throwing codes.
Isn't your CAT welded to the downpipe? Is you new system flanged like the factory system? If so, you could try re-installing the downpipe with the CAT in it and see if that corrects the problem.
While it may be a secondary issue for you right now, recent edicts from the EPA would suggest that diesel emissions testing is coming to an area near you as it has here. Re-installing the CAT, or at least having it available when needed might be a way to go. At least I'm going to try CAT back on mine and see what kind of temp changes, if any, I might get.
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