Are you on dry pavement when this is happening? If so your not supposed to do that, only use 4x4 when the roads have snow or offroading in dirt or mud.
Are all the 02's reading bad or just the front or the rear ones?
Were NGK O2's installed, they are known to be the best.
Does the JK still have the Factory Cats?
Bad, dirty grounds can cause alot of issues along with the junk Factory battery clamps.
The Factory battery clamps are know to be junk, replace them with HD ones.
Do you have 12v's now at the new battery? Check to see if you also have 12v's at the starter on the battery cable.
It's a Throttle Body that's for the engine in the Dodge Viper car, it's a little bit larger then the Factory JK's one.
There's lots of info on it in the other JK Forums.
I put a Viper TB on and then 2 times after that I got the lightening bolt. I searched for a fix and found the TB reset and after doing it the 2nd time it worked and that was about 6 years ago.
That seal leaking slightly won't cause that noise, did anyone check the oil level?
Bumps causing the noise and vibration would be shocks, wheel unit bearings, skid plates.