Yes, all 1996-2004 Tacoma and 4Runner Transfercases are the same, as far as function and internals go.
As for a comparison with the older 1988-95 V6 t/case, a while back, Marlin spoke to the person who redesigned the VF t/case and learned that the chain was widened and also features an increased number of links.
Please read this thread for more info:
What does Marlin really think about taco tcaseRegards,
BigMike
