How I believe the cars work is there is a reed (magnetic) switch in the dash itself, which is driven by a physical linkage (you can see the square cable that slides into the gauge cluster - I'm sure you've seen this). Reed switches are easy to damage with improper signals so if you have messed around too much it's possible you've done so. I personally see no reason why your stock speedometer shouldn't work, unless you have removed too much of your original harness. It does not appear from what I have read on the links you've given me to be driven by the stock ecu. The stock ecu just has a input for such things as cruise control, and idle control. ABS systems use the vehicle speed sensor too, but they are also a seperate unit from the ecu. So basically you should have 3 seperate systems that use the vehicle speed sensor, the ecu, abs, and instamentation. There are unfortunatly no schematics in the pages I've seen on the electrical manual, so I cannot tell if and how they are spliced together in any way.
On the link you posted up there, it shows the stock vehicle speed input to be pin 45 into the ecu. I presume you removed your original harness, and the speedometer worked flawlessly prior to this install? How much of it did you remove? You should try and trace what you did and see how it branches out behind the ecu to the sensor. Again, when I get home I'll try looking at the haynes manuals for my turbo 1g, even though I have no ideas of the difference between the 1g and 2g.