Sorry the the late reply! What exaclty is it doing , or not doing ??
But to answer your last question a the 2001, NO it probly will not work in your 99 without taking it apart and swapping some parts.
Reason being the gear ratios changed from year to year, and a few other things are different.
Problem with the 99-02 is a plate gasket inside on the VB isnt made right, and leaks internally, along with the pump shafts are to small and prone to wear/break prematurely.
You might be better off in the long run if you get your trans rebuilt.
Price for a used trans plus install could cost between $1600-2000 depending on where you live.
A rebuilt one about $400-600 more, but worth it if you love your car.
Here is a thread i posted when I rebuilt a couple of the 4T65E's in 2007.
http://www.automotiveforums.com/vbul...d.php?t=708108