In terms of the saddle, you clean/treat it best you can, lotsa great suggestions here. Try the ones that are practical, like I'm supposing traveling to PDX to visit Langlitz ain't. Whatever comes out the other end adds to the saddle's character.

In terms of future prevention, I'd give a big YES to the idea of not doing more long-distance rides in nylon shorts. Not to get too anatomical/personal, but I'd be worrying about my own hide's scuffs, not the saddle. But I'm biased from having to prove I was a serious cyclist back in the late-'70s by wearing real bike shorts, when a Brooks Pro was standard equipment.

For shorter rides in nylon shorts, and for longer rides in bad weather _wearing actual bike shorts_, a cover is a good idea. Doesn't feel as nice as no cover and actual bike shorts, but should minimize saddle damage. For wet weather either a rear fender or making sure your cover protects the saddle underside is a good idea.

Might be worth saying that in some circles, a pair of non-cycling shorts/slacks with a Brooks ass-stain is a mark of honor. So there's that.