I had a 2000 mustang and it had some dash rattle as well as all my Camaros and Trans Ams. I don't think your ever going to get away from it and just something that happens on these cars with age. At the end of the day these are cheaper cars that are made to go fast opposed to offer a luxury ride.
I have an 06. My car has the dash rattle and the same hesitation between the mentioned gears. I have to drive a brick road on the way to the gym. The dash rattles on that road quite a bit. Sounds like static on the radio, but it's the dash. Guessing its normal rattle due to vibration from the road.