Recently noticed a rattling noise which sounds like it’s coming from the front/ can feel it in brake pedal. Only happens when coming to a stop but if I put it into neutral when stopping the noise does not happen. Any ideas what it could be? I checked the flex plate bolts and they were all tight.

2000 4.0 AW4

 

Classic symptom of a loose or cracked flexplate. The torque converter bolts might be tight, but the flexplate itself can crack around the bolt holes. The noise goes away in neutral because there's no load on the plate. Pull the inspection cover and check the flexplate for cracks, especially between the bolt holes.