My recently purchased '98 xj shows just the beginnings of rust developing in the rocker panels on both sides. What I'm doing & I hope it works is to drill 1" holes into the panels from the top (under the plastic threshold protectors), applying POR-15 to the worst spots at repaired rust-thru sites, then will be spraying used crankcase oil into the panels via a pressurized garden sprayer. I have blown out a lot of rust & grit from the panels after I drilled the holes to clear them as much as possible first. Don't know if this will totally solve rust inside there, but should certainly slow it up if done occasionally.
regards,
jlex.