96 contour problems

ok i got a 96, with the 2.0 dohc, automatic trans and thats were my problems are at. i recently had a oil pump gasket leaking and had to lift up motor and trans to get pan off.fixed that leak but now tranny won't shift and spedo doesn't move at all.shifted fine before and spedo worked but o/d off light came on but you could push the o/d button and you could hear in downshift. took it to ford and they said it was internal but i find that hard to believe since it worked fine before.so my question is does the vss tell the pcm when to shift? and where is it located? any help would be great trying to get rid of this car and for some reason she just doesn't want to go thanks in advance