What do I do before I ship a manuscript? You mean besides panic over the fact that I'll never catch everything? That the MS will never be perfect, even after (if ever) it's published? Yeah. That happens first.
Then a round of deep breathing later, I run through a series of checks - ones I know are issues for me.
1. When I find a phrase or a gesture I like, I run with it. Everywhere. For everyone. I get to flip my hair out of my face. You get to flip your hair out of your face. EVERYBODY gets to flip hair. So there's a search for repeated gestures, phrases, and words. Most of this gets caught during critique. If not, it gets caught during dev edits. if not, the copy edits. But, if not, the buck stops with me. So, yeah. There's a final read for that nonsense. I do my damnedest to repeat the same physical character gesture no more than three or four times within the same book. Try.
2. Continuity. Continuity. Continuity. It's my own personal pet peeve, meaning I'll cut everyone else all kinds of slack on continuity errors, but my own make me insane. True story: A certain novel made it through several crit rounds, dev edits, copy edits and was sent to me in galley for final approval. Lo and behold. Continuity issue. My heroine was having a conversation with a hero who was unconscious and in surgery at the time. Oops. The house didn't charge me for fixing that - they could have. Second true story: there's a short story out there in the world that is rotten with continuity issues. It was picked up on an emergency basis and on a super short deadline when someone had a hole in an anthology. The editorial pass was super quick and the turn around so fast that I missed all kinds of problems. You can subsequently drive entire solar systems through the gaps in that story. To my eternal relief, I got a do over on it. It's MUCH better. Cleaned up and out there in the world for free as part of Tales from the SFR Brigade antho. No. I am not going to tell you where to find the tragically broken version. You're on your own there.
This proves the adage you likely heard from your father the way I did from mine: If a job is worth doing, it's worth doing right.
In the case of final passes on books, it means TIME. You have to have enough time scheduled to give yourself the time and space for a careful read through your book after it has settled sufficiently into the crevices of your brain. You want to be able to read the story without being caught up in its brilliance, but also without being stumped by every little typo you spy. Or finding out that no one caught the fact that the hero seems to have three hands in the love scene (and he's not an alien who's supposed to have extra appendages). You'll have to fine-tooth comb the text for your particular issues - we all have them. And they're all different. So I can tell you that I have to search my MS files for --! which is how you comment out code in SQL. Old habit. But in a story, when I want to mark something for future clarification, it gets commented out. Jeffe has to search for her brackets, I search for dash, dash, bang. You'll have your own tic(s).
Each book is its own entity with its own gotchas and pitfalls. My final tune up list varies depending on the project. But finally, there does come a point where I have to stop fiddling and release the thing either to fly or crash and burn. I make the appropriate sacrifices to appease the Book Gods (or demons, depending on your day). I hit send. And promptly find three typos in the first two pages.