bent input shaft? usually input shafts can twist, but that's usually with a good amount of power and some really sticky tires. and when does it make the noise?
EDIT: i just saw you're pulling 12.50, so it very well could be a twisted input shaft. i would go ahead and upgrade the whole transmission while you're at it, whether it's a rebuild, or a new tranny. do it right now, so you can throw more power at it in the future and not have to worry about it.
2002 Procharged GT
12.503 @ 113.08