noises in shifter

Does the car have an aftermarket shifter? If so, it's normal.

Transmissions are actually pretty noisy. The reason you don't hear much with the OEM shifter is the use of a rubber isolator in the shifter itself that prevents alot of the gear noise from making it into the cabin. Aftermarket shifters do away with the squishy, rubbery isolation to get a crisper feel and the penalty is more noise.

If it's still got the factory shifter and you've noticed the thing getting louder, you might want to check things like the trans fluid level and the rubber isolator in the shift handle.
 
Noticed that after my B&M shifter install. Definitely a little more tranny noise getting into the cabin now. I hadn't even thought of the noise being from the shifter until reading this. The one-piece aftermarket shifter probably DOES transmit more noise than the 2-piece OEM one.
 
My trans did seem like it made more noise after my steeda shifter install probably because you have to cut the factory boot.

Heres an interesting product I found the other day that MGW sells. Anyone have one yet?
http://www.mgwltd.com/mustang_shifter_inner_dust_boot.shtml

The benefts are many with this new boot....
1. It is not as stiff as the factory second inner boot that some guys are putting on the MGW shifter. The one that is connected to your factory shifter.
2. Allows the picture frame inner boot pictured above to seal the base of the MGW shifter from all dust and moisture and also reduces road noise by a good amount.
3.The MGW boot SEALS the top of the shifter from any dirt or debris and also still gives a nice free feel to the shifter. It also muffles road noise and tranny whine coming up from the shifter.