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Hello and welcome to just answer. If the noise is vehicle speed related and not engine RPM related, then it is most likely a drive shaft/U joint issue so start there. Have the U joints and drive shaft inspected closely. I doubt it is in the transmission itself, but may be transfer case related. If a visual inspection reveals nothing, then have the Jeep put up on a hoist so it can be run in gear while a technician uses a mechanics stethoscope to help pin point the source of the knock.
Hopefully my suggestions will help you narrow this down.
If flywheel bolts were loose, then the knock would be engine speed related. Run it up on a hoist and use a stethoscope.
I understand, but I cannot touch, hear or visually inspect the vehicle. You have to be my ears and eyes, etc. I can only suggest what I think it may be. If this were a common problem with TJ Jeeps, then I would tell you what I have seen in the past. I hope you understand and if you want a refund, then I totally understand.