Absolutely the best way to do this is to record everything in Multitrack. For a start, it's direct to disk so if anything goes wrong, you don't lose everything. The other thing you should do is not to alter anything about the way you are recording, between takes. Get it set up correctly first, so that the number of things you need to do is minimised. Then, without altering anything or doing any processing, edit the takes together in multitrack so that you have a whole segment (say, a chapter) that all sounds the same. You make a note of all the settings on everything, and then process that chapter as a whole by mixing it down to a chapter file and processing that in Waveform view. Why? Because you need to make a note of all the settings you've used to process the track (save everything as presets, or even set up a Favorite if you want). The reason is that when you come to do the next chapter, with care you can use the same presets. Yes, you have to watch out a bit with NR, but even that can be replicated if you save a noise print, and create a preset for the processing. The other important thing to note about doing it this way is that your original multitrack (unprocessed) edit remains intact, so if you need to, you have something to go back to.
Doing it this way means that you should end up with consistent results, and if you need to go back to anything, it shouldn't be too difficult. It's all about having a processing structure - once you've got that sorted out, and you can stick to it, the rest is pretty easy.
It's good that you've realised that breathing makes speech sound natural - it really does make a difference in long-form recording to have a natural-sounding voice. It means that without effort, the listener should be able to have a more 'immersive' experience - which is of course what I would have thought most people wanted from an audiobook!