It sounds like you have embarked on a territory that requires quite a bit of braille formats training. NIMAS files are extremely useful tools in which to begin transcribing a textbook, however, as a transcriber, there is quite a bit more involved than simply opening a file into a braille translation software. Managing a textbook transcription can be a daunting task, for even the most experienced (certified) braille transcriber. You are absolutely correct, there is a great deal of clean up required. The translation software will open the file and translate most of the text into a clean braille translation, but formatting experience is a must for proper transcription of a textbook. If you have not downloaded Principles of Print to Braille Translation, 2016, I strongly suggest you do so. The formats book is a guide for transcribers to use to format textbooks. This book is free to download from BANA (Braille Authority of North America). The guidelines may be downloaded from the following link: http://www.brailleauthority.org/publications-area.html. The BANA website is a wealth of information. Not only can you find code books, but there are endless documents on UEB (Unified English Braille). Nemeth, Foreign Language etc. Are you literary certified? If not, a literary certification is where you should begin. The National Federation of the Blind offers Literary Braille Transcribing Courses and certification, and this is where you should begin your process. The link to NFB Literary Braille Transcribing Course is: https://www.nfb.org/programs-services/braille-certification/literary-braille-transcribing.
Posting your question on the NBA website is a huge step in the right direction. Are you needing training? NBA offers on-site, personalized training upon request. There is an online form under the What We Do tab on the home page of the NBA website main page. You can find the form under Training Bureau Inquiries.
As a member of the NBA, you can also access the full Webinars Archive. You will be able to view videos of short trainings on various aspects of braille: Braille Formats, Foreign Language, Nemeth, Music, Tactile Graphics, UEB and more. Members can access the Webinars by going to the NBA Homepage and clicking on the Resources tab. From there, just find Webinars and the appropriate category that interests you. I hope this has enlightened you and just know that we are always here to offer advice and assistance. Please let me know if you need further guidance. I will be happy to point you in the right direction.