On the '99 3RZ-FE, you have three choices. There are two inputs from the VSS, one on a purple/blue wire on Pin 9 of Plug C28. There is also a green/blue on Pin 1 of Plug C28 that goes to the ABS ECU. It seems it goes through a resistor in the VSS.
Then there is the Speed sensor output on the green/orange wire on Pin 3 of Plug C28. This goes all over the place, including the ECM, 4wd ECU, Cruise control ECU, and A/C Amplifier (control.) I'd probably try this one.
Plug D is a blue two-row plug with 12 pins on the back of the gauge cluster (Combination Meter).
I only have this one in paper, otherwise I'd post it for you;this 2000 looks the same. VSS is on left side of first page.
Pin 3 of the VSS has a white/green wire. The best I can tell it goes over the transmission to the bundle near the starter, back behind the engine, through the big firewall grommet on the passenger side, and then back around to the back of the cluster. I'm thinking pulling the cluster is going to be the best way to find it?
This is a non-ABS model also
Well, the only thing I can tell you about routing is that the VSS wires go through the II3 connector which is behind the glove box connecting the cowl wiring to the engine wiring. II3 is a big white 4-row connector with 26 pins. To get to it there, you only need to pull the glove box. I don't see a white-green wire anywhere for the VSS. No idea why you have that. White with green is usually part of the illumination circuit.
And you're right, the ABS connection I mentioned is asterisked as 5VZ-FE only.