Been there, done that, they never gave me credit for the returned part.
I pick up one from the local Jeep dealer. The part is from a TJ. It was a perfect fit.
This was on ebay.
http://www.ebay.com/itm/OEM-Jeep-Wrangler-TJ-Manual-Transmission-Inner-Shift-Boot-97-04-Shifter-tear-/221198231609?pt=Motors_Car_Truck_Parts_Accessories&fits=Make%3AJeep%7CModel%3AWrangler&hash=item3380712839&vxp=mtr