It doesn't sound correct that two of the lines remain the same all the time.
I know there are several ways of wiring this trans, depending upon what year it is.
I think the 95 was OBD 1.5 (interim step between the old OBD1 and the new OBD2) so there may also be some strangeness associated with that.
Be sure of your wiring, and the year of the trans and ECM. Make sure that any chip that you have made is compatible with your setup. (The 4.9 has like 5 or 6 different tuner "vehicle definition files". There seems to be no rhyme or reason as to what file works with what year or options, other than the broadcast code on the chip. Seems like it would be easy to get confused.)
What is the broadcast code on your chip? Should be a 4 character code. BWYB, AUXW, etc.
be on a label on the ECM as well, but that doesn't necessarily mean that's actually what's plugged in. They're easy to unplug and swap around.
[This message has been edited by Raydar (edited 09-11-2013).]