trans rebuild question

So i have a 2001 GT mustang with only 46000 on it. the trans has developed a shutter between 2nd and 3rd gear. I,m not sure a lot about automatics since this is my first stang with one . I'm wondering if i will most likely need a full rebuild of the trans and if so how much do shops generally charge for this ? Also seems weird it would happen with such low miles so i was also wondering could it be something simpler and cheaper then a full rebuild. thanks.

I did have the fluid and filter changed at around 35000 . i haven't driven it yet this year yet since the weather is crap here (wisconsin) , but as I remember it only happened if I was driving regularly not if it was under a load / under higher rpm's . I believe it was only when the car was going from second to third .