Okay, misunderstanding.
So it was making this noise, you replaced the transmission and it is still there.
I would start with a good visual inspection of the exhaust, and engine mount areas, if the exhaust system can move and hit the body or you have a bad engine mount, both could transfer engine noise to the interior.
If it was an internal engine problem I would expect it to happen all the time when it hits a set rpm area. But it does not seem to do that.
The CEL is not on correct?
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Friday, November 24th, 2017 AT 10:15 AM