Hello, I like what you are doing kobushi!
A friend of mine and I were going through a set we had gotten online and renaming them to some Tosec standard. The HDM and NFD decision sounds great. HDM I am not familar with but that sounds awesome since it is widely compatible and a generic format. Also while going through what I had I did notice that some games would work in NFD but NOT D88, so again another good choice.
My thoughts is that you can just take what you want to include it in your set, since it sounds like you are going through a huge amount of files, (64K!). Here, all the .hdi and the non-alternates were tested to be working. These files are renamed mostly using the transliteration from
http://fullmotionvideo.free.fr/screen/%21title.html. The files I am posting seem large, but keep in mind two things. One I have lots of alternates, so I just renamed them or whatever and put them in. The .hdi s I have been using are probably over large, since I do not know how to determine the needed size of an hdi, nor do I know how to modify the size of an hdi after the fact. I have been installing every game so far that has needed it, and tried to make them auto-boot if there was not already one that did this. The games that were just loose collections of files were put together in an hdi and made to autoboot when possible The most missing company alphabet letters are mostly from 「こ」「て」「ひ」「ほ」「ゆ」「り」since that is pretty much where I had stopped last time any time in this. Also if a game seems to have another disc it is because I included a User Disk since those things can be pain to make and many games will not even be playable without one.
So do what you wish with these, it would be nice if they are helpful in some way.
https://mega.nz/#F!VnZ1yJKT!UtF7vaRpvOFhmc-8uE4u9QIf there are any issues with my uploaded files tell me please.
To be honest seeing you do this is a bit of a relief since I was kind of getting tired of seeing all the hentai games.
edited: 2017 07 24 8 PM - Posted my home link instead of folder link. Updated. Please try this.