When you say between, you mean the normal position on the transmission output shaft? On the top back of the transmission?
FWIW, the improper shifting is a side-effect of not having the correct speed reading on that van (well, it is on a 99).
The fact that it seems like you are getting two different rates of signal out of the vss seems odd. It makes me wonder if there isn't something physically broken or dirty on whatever drives the magnets past the sensor. Since it's on the top, you'll need a mirror or a camera to look into the hole, but you can generally see the sender rings go past if you look in the hole with the sensor removed.
I would also talk to whoever changed the output shaft. (At least on the 4r100 that's pretty involved.)
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'99 EB ex ENG KSWB news van, low rent 4x4 conversion (mostly fixed by now), home built interior.
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