Reason I ask is I plan on using that trans (2003 5r55e) in a 1999. The 99 doesn't have that connector.
I am hoping that since the 99 has the VSS sensor on the rear diff that I don't need the ISS sensor.
The ISS sensor is used for the adaptive shift control, not for the speedo (software changed in 01 and got more complex which is why they added the ISS for more feedback). As long as you use the 99 computer it should be fine without hooking it up (I think).