Yes, exactly, sounds like your (possibly aftermarket) antenna is connected to some alternative controller and not to the factory wire harness. As shown in your engine bay photo, the '97 Land Cruiser factory antenna motor cables have two connectors, one 2 pin connector for the motor, and a 3-4 pin connector for the antenna position feedback to the controller. In your photo these two connectors are dangling there and not connected to the antenna... The mods you made to the control module only affect the factory antenna motor connector. The factory 60050 antenna uses only the 2 pin factory harness connector. (I again tried to mark up your photo but for some reason IH8Mud won't let me paste or import images to this thread... Weird.)
You may be able to somehow connect your antenna to the factory connector, if the antenna has two wires for its motor available... In your photo I see only a red wire that looks spliced to a blue wire.
