Really depends on what is not hooked up now? Overdrive is part of the transmission, not an add on. So for any shifts to happen, you will have overdrive also. If it isn't powered up, hooked up, etc, all you get is 2nd gear (with no engine braking) and reverse. Those are the fail safe mechanically selected gears.
Since you stated it has the Baumanator in it, you may not have an old enough laptop to connect to it. You may need a USB to Serial adaptor. Since those were programmed via the serial port. That's about the only hardware that may be needed now.
Can always start with the basics. Is everything plugged in? Does the light come on when powered? Does it have power? Have mice eaten the harness? Was it ever hooked up in the first place?