Could also be-
Windshield wiper shafts loose and need new caps w grease in them
Plastic sheet between door and inner door panel needs sealing
Door seal on body
I thought I'd never sell my OCD maintained 4Runner, however I just picked up a 2010 LX570
Link to picture album-
https://www.flickr.com/photos/182144991@N08/sets/72157709133452436/
225k miles
Legendary 4.7 V8, with the 5 speed auto transmission- essentially the same AWD drivetrain as the 100...
Check this out, I think it would look much nicer, and still give you more clearance.
https://www.g-wagenaccessories.com/products/rocker-panel-guard-for-lwb-gwagen