I used SqueeBooks a few times for LJ fics but it kept giving me very bad results so in the end I simply copy-paste it all with patience on a document and then do the formatting and TOC and all myself. It's faster after a while.
re ao3 tags
Spoiler:
I personally don't let AO3 import any tags on my calibre library and input them myself. AO3 canonical tags are awesome, yes, but redundant (for me). Plus all the extra are too many and too different depending on the author. So I import and leave all blank and add myself by reading the tags .. Like if in ao3 is "angst, hurt/c, romance, I was drunk, friends to lovers, case fic, lol this was cool, france, medieval, torture" I put my "H/C, Case fic, Place.France, Past.Medieval, Violence" I feel it's more organized. After reading it I usually add or delete tags accordingly, like, if they also went to Africa, I'll add that. It doesn't take time at all, I know my tags, I know what I can add, so it's a matter of seconds.
I also don't care about the F/M, F/F, M/M etc because 90% of my fics are M/M (and the same pair) the rest Gen and some F/M and F/F. Plus the whole library (3000+) is only for 1 fandom so no need to add that or the characters. Probably if I start reading another fandom I'll create another library. The organization of our libraries is very subjective, it depends on so many factors, in how many fandoms you like to read fics, your favorite tropes, if you have otps or not...etc. All that would shift the building of the library and the tags involved.
For kinks i have "Kink (general one), Kink.BDSM, Kink.Omegaverse, Kink.Voyeurism" and that's all, I don't really read many kinky fics, no D/S, no heavy BDSM etc, so that's enough for me, I have very few.
I do love to nest tags. I do it for Job AU (Job AU.Coffee etc), for places Place.Italy, etc, for Supernatural elements (Supernatural.Magical Realism, Supernatural.Vampire, etc) for Sci-Fi like Sci-fi.Androids, Sci-fi.Dystopia etc, for Eras "Past.19th century, Past.Regency" ...and others.