On your antenna not retracting problem, I recently bought a 93 LS 400 and it had that same problem. The antenna mast was "kinked" near the bottom under the chrome bezel so you couldn't see it at first. The antenna is raised and lowered by a flexible nylon "toothed" rod that goes up and down inside the antenna mast. The nylon toothed rod is coiled up inside a round gearbox on the antenna base in the trunk. I purchased a new mast from Lexus of St. Louis, Mo for about $60 and repaired the antenna myself. On my antenna, when it tried to retract, it bound up because of the kink and the retract motor snapped the flexible nylon rod, leaving most of it coiled up inside the round plastic gearbox. I had to remove and disassemble the antenna gearbox to remove the bottom part of the nylon rod that was coiled up inside. Once that was done, it was just a matter of feeding the new antenna mast into the antenna base with the retract motor running in the retract direction. The Lexus repair manuals go into some detail on how to do this. Good luck.
Curt