Welcome to the Z. The computers in these trucks don't like it when the sensors aren't working right. Unplugging them which cleared the problem certainly shows that's where your problem lies. I've heard there are ways to fool the computer into thinking they are there, but I can't remember the way to do it.
As for the stripped out "nuts", do you mean you rounded off the sensor? Normally that's what happens. If that's the case, try soaking them in penetrating oil over night and use vise grips. If that doesn't work, take a torch to the thread area to expand it and then work them back and forth with the vise grips.
If the threads in the pipe are stripped then I suggest boring them smooth and larger then tap them and put in an adapter which fits the new sensor and is the size you need for the new hole on the outside.
I doubt the sensors would work correctly if they are to far out of the exhaust stream.
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