In my opinion I would drill and put a new sensor in the manifold. From my experiences factory instrumentation can seem to vary some from actual numbers. I do a lot of work on big diesels, Mainly cats, and a pyro probe on those can vary 250 degrees from the ECM reading through the laptop.
Your BADP exhaust will throw off the readings from the stock probe. You have to drill and tap the manifold to get an accurate reading. You also need separate software to use a standalone probe with the 6.7 PMT.
It is still technically in beta form. You need to get the software from the vendor you purchase it from or from Bully Dog. I have the new software for the pyro; it is now part of the latest PMT software. It still does not have the ability to clear codes on start up.
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