I should have used LaTeX from the start, yes. Manning accept manuscripts in LaTeX, moreover, they prefer to work with LaTeX formulas, and even if you write in MS Word, there is a pugin for LaTeX that they encourage you to use...
...and I learned all of that after the manuscript was done. That's on me, I should have been more inquisitive. Also, I should have asked about their style guide and technical requirements for the graphics. The book was supposed to be ready for printing sometime this month but now the launch is delayed till June since they have to redo 300+ graphics from scratch.
Self-publishing definitely gives you more freedom. But Manning also give you a development editor, a technical editor, a copy editor, a technical proofer, a copy proofer, plus a few dozen reviewers, and a whole production team. Writing for a publisher does feel like a deal with the devil, true, but it is not that bad of a deal.
If you want, write me a line (ok@wordsandbuttons.online) and we'll chat about publishing with Manning. Or without. My first book was published on Leanpub, and the second is available from wordsandbuttons.online directly.