As I'm doing query critiques for a conference, I'm reminded that it's often the simple things that make the most difference.
Use an easy-to-read font like 12 pt. Times New Roman. It makes a big difference.
Melissa Edwards @MelissaLaurenEI literally just got to the end of a query that sounded interesting (was considering a request) and the P.S. is the author insulting literary agents... why would a person do that
If you can't eliminate that scene, find ways to cut and make what's left more vivid and emotionally resonant.
For scenes that were out of order, take a close look at your plot. There's a reason you didn't remember it correctly.