More Plot Holes Filled:

Time passes quickly in my '100 Waifus' novel, and obviously conversations and events occur off-screen as often as on, but I decided to move one conversation 'on-screen' to clear up confusion as to what people knew and when did they know it.  The clarifying addition comes at the start of chapter 3:

　　After two weeks of Sakura-based construction and manufacturing everyone had been able to move in to their new rooms enjoying modern amenities. Life was at least up to 1950's standards for all. It was at this time I explained to everyone who they were, how they got here, why I appeared as a different special person to each of them and why I seemed different from their memories.  With so many obvious holes in my cover story I didn't think lying would get me very far, so this was less a cherry tree moment and more a matter of necessity, but surprisingly they all took the truth rather well. With that out of the way, the next step was expanding our residential district into a commercial, civic, recreational and industrial district. My waifus tended to be passionate in the pursuit of jobs or hobbies so there needed to be a space where they could be themselves if I wanted this village to truly approach the standards of 'Paradise.'

By making things clear to everyone so early on, it shows why Christopher's conversations with Yukino, Rydia, Haruka Haruno and the rest seem to already be aware of all the ruses played on their lives.  It also explains the sentence about how Christopher was tired of lies and didn't want to wear any masks.  This was obviously his explanation for why he gave an explanation.  But without the explanation explicitly being explained to have been given, the explanation for the explanation makes little sense.  Thankfully everything has now been explicated.

The second plot hole was filled while Christopher was conversing with Mirajane:

         "Should a grandmother and granddaughter really be having sex together?" Mirajane asked.

　　"I'm already married to multiple blood-related sisters so I think that ship has already sailed." I said with dead eyes.
        "Including me."  Mirajane pointed out.
        "Including you?"  I repeated in surprise.  Mirajane nodded wordlessly in confirmation with a look of composed neutrality.  So Elfman had been her most special person.  I could have sworn it would either be Makarov or Laxus. . .

　　"Dear, have you ever thought about seeing a therapist?" Mirajane asked plainly, clearly not as into incest as I was.

　　"This is what every normal healthy boy feels in his heart." I said in a zen like state.

It wouldn't make sense for Christopher to bring up the subject of being married to sisters without Mirajane pointing out this applied to their relationship as well.  The previous 14 versions of the script she let this comment pass over unremarked, but now she's done so, which makes explicit why she's so hard to get later on in the story despite the two of them spending more time together than practically anyone else.

I also correct a later conversation with Sagiri that used to include Illyasviel as a blood related sister while excluding Mirajane.  Actually Illyasviel is just another foster sister in Fate/Kaleid Liner and thus I deleted the sentence mentioning her, while Mirajane is the real deal so I added her in.  Accuracy is essential!

As I read through my novel for the 15th time, I'm also correcting minor grammatical errors -- like replacing an 'and' with a 'but,' deleting extraneous spaces, etc.  Hopefully this will be the last read through necessary to correct all the pointless mistakes and fill in all the confusing plot holes.  But I'll keep doing this as many times as necessary until I find nothing left to correct.