Appears to be a bit more to it.
That R/W wire from the Auto isn't used in the 5 speed.
Instead, a R/LB wire from the ignition switch "Start" position sends 12v to the electronic shift module.
Then, over in the Cruise Control, the clutch switch takes a LG wire through the clutch pedal switch contacts, routing 12v to that Cruise amplifier while the pedal is released. If you still have the auto transmission's harness installed, the jumper will be completing this circuit and is NOT part of your problem.
Catfishdaddy, if you send me a Private Message with your e-mail address, I'll send you the 93 schematics to show you what I'm referring to. Since we don't know what you did or didn't do with harness/wiring, it's hard to guess your problem. If you did NOTHING with the wiring yet, you'll need these schematics to do it properly.