Denver - Meet your Lexus's Kentucky Cousin... I purchased the exact same trucks (1998 with 237k on the clock). Mine is the same rare color (Smokey Topaz Micah). I had similar rust issues. I can talk rust all day long! Mine was mainly on the undercarriage and four corners. Rust is the enemy... get rid of it where you can, cut it, sand it, paint it. Get rid of it! That being said here is my rig. The body panels are done with truck bed liner.
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I started at one end and went completely through mine. There are some good things about a rusty LX - it will never be "cherry" so you can have some fun. I would have never painted body molding on a pristine LC or LX, I just wouldn't! Once you've been liberated by the rust... you can get to playing. I'm so glad I used the bed liner... and the results are amazing!
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CUT IT OUT! The great (or really bad thing) about the LX is body panels cover most of the spots that are prone to rust. I shaved 2" off the bottom of the rear passenger side corner, wedged in some foam core behind for support and through in some fiberglass. I'm eventually mounting a ladder here so the ruff body work doesn't matter.
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Again - not perfect but the "spot" is now coated with bed liner and will eventually be covered by a low profile tool box and ladder.
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Pay close attention to areas where rust will hide. I'm telling you now, rust will be in places you never imagined. I spent a month "de-scaling" my undercarriage with a drill and wire brush. The good news is things can look horrible when "scaly" with rust, then will clean up better than you thought. Learn to tell the difference between "brown meddle" and "cancer." Surface rust cleans up easily and in some cases isn't even necessary to address right away. Though I treated and painted everything with a rust preventive / converter even if I planned to revisit the spot later. In my opinion (and that is based on my experience alone), it's better to get it treated, ground down, sanded... whatever it takes, then put some Rustolium on it. Even if you plan to come back latter... stop the madness. The added paint will help you ID surface rust from cancer later. DO NOT JUST PAINT RUST - this is not what I'm suggesting, at least treat it. But best case, grind it down and at least get some primer on it. I'll post more on my build later - good luck!