You SURE its coming from the trans and not an accessory on the front? If its a lower pitched whining it could be the trans on the way out. Does the noise change at all or go away with clutch pedal action? The TOB will generally sound like a higher pitched squeal. The 96-98 transmissions are notoriously problematic when they get up in miles. In 99 they were much improved.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.