I'm so sorry my reply has taken a lot longer this time >.< I've been super busy with work related to my other project, CiQ, haha. My good friend Anthony is helping me with casting and the audition deadline was last week so he sent me lots of auditions to listen to. We spent the week trying to pick the final cast and I was preparing scripts to get sent out to em :3 Can't believe how much time has passed already, it's like the whole week just flew by! Haha. Anyways, I shall go ahead and get to replying now :D

SPOILERS

Although you don't see the pairs being tested other than the ones you play as, there are other lab workers + test rooms all testing various pairs at the same time. So while you're playing as MC, there are loooooads of other pairs being tested by different people who aren't as important/high ranking as Raine. Raine and Isaac tend to just work with whichever pairings are showing the most potential (not always though cos sometimes they go on tours of the lab and drop in on other workers to check on their progress and stuff) :3

You're correct about if a pairing is successful they will be used in another route :3 The number they have is just kinda like their model/factory number though. The lower the number, the older the body. So 26's body was pretty old and had been through a lot x3 The fact that they put part of 26's consciousness in 339 is supposed to sorta show how many MC's they're going through cos they go through em in number order, and the next available unit to wake up was the 339th unit in the lab. As for Kuro, the one in the training room would remember fragments of what happened during the simulations, but more importantly, he remembers what is happening outside of the simulations. They let him remember on purpose so that he's easier to break >.< And the one that you see with 26 is pretty broken :( He wouldn't always have been like that, but all the years of knowing that the simulations are more like a dream/escape and then having to face the horrible reality he's stuck in really wore him down.

When he talks about having explained to 26 over and over, he means that he's tried to get her to remember/understand that the simulations are exactly that, and that where they are right now is reality, but because they always take that information from her, he was never able to successfully get her to see that truth. So in the end he just gave up trying :(

I only called her 26 cos it was my age at the time of writing her part of the story :3 I tend to think of her as the heroine of the 5 main routes also. I'm 28 now, haha.

In the simulations, Isaac would have wanted physical feelings and sensations to feel as real as possible, so I'd say that they're probably stringer than the sensations of a dream, but not quite as powerful as how they would actually feel in reality.

As for the creepy voice's reaction to the ending you picked, yeah, he doesn't like it if you pick that one x3 But it's okay, they're safe, he's basically just throwing a tantrum and showing you what he thinks of sweet things/threatening you, haha. There are some slight changes in his dialogue at the end. He says something slightly different for each choice that you pick during the conversation with him + he has one slightly different name if your player name is Anathema :3

I'm glad you liked S****'s sprite :D I thought he was the best looking one too x3 I went a little crazy adding all the belts to him xD I kinda wanted to make him look like a Final Fantasy character, haha. I love detective Kuro's hair x3 it's all flowy kinda like he's underwater :D His body looks super feminine though with it being in that tight outfit >.< haha. I mean his sprite body is technically just a flat-chested female body xD There are nowhere near enough sprite resources around for male bodied sprites T_T Oh gosh, I think all of the Kuro's drawn in Mei's art style would have looked incredibly gorgeous cos the student route one that she drew is HOT x3 haha.

As for floating, I can't actually remember x3 I don't think I had mage or gamer Kuro floating. I hadn't really decided for student Kuro, but I don't think I referenced him floating. It was more just something I thought would suit the detective one that anything else :3

The clones are fairly close to human, yeah :3 Not quite 100% since they've been manufactured in the lab. They have certain alterations to their bodies to make them more durable and stuff, but for the most part, they have flesh and bone like you say. They don't really need to eat, but they able to process food. If any of the Kuro's were gonna have a sweet tooth I'd say it would be the detective and gamer ones :D I can imagine the gamer Kuro just innocently sucking on lollipops or something x3 and detective Kuro with his candyfloss, haha.

In regards to mage route Kuro being indecisive about where MC should go, that version of Kuro is the most sorta split between wanting to help MC and wanting to destroy MC x3 They pretty much have ended up with a split personality and try really hard to keep it under control with the route. The indecisiveness is Kuro having an internal battle between the two personalities. The unfortunate bad end that follows is what happens when the twisted side of Kuro comes to the surface and defeats the sweet side x3 So you're exactly right when you say it seemed like there were two Kuro's in there! By that point in their story, poor Kuro is already pretty messed up from years of going through what they have. The Kuro in the 5 routes is always struggling internally to keep the crazy part of him locked away, but in the mage route, he just doesn't do a very good job of suppressing that x3 

Yeah, a lot of the music on Incompetech is incredible :3 I couldn't have asked for a better library to choose from! Almost all of the tracks came from there aside from the odd few that came from Purple Planet Music and then some that I own from a music pack I bought many years ago, haha.

The Kuro's kinda treat the simulations as a holiday when they're worn down, because getting to live that life is better than life in the lab, so in a way, it's like a breath of fresh air for them and they enjoy the 'freedom' that they have there compared to what they get in the lab. Kinda like if your whole life is a nightmare, you're gonna prefer a having dreams to facing your nightmare reality x3 When they're fresh Kuro's, they're less aware of what goes on in reality, so they treat the simulations more seriously like they really mean something, whereas the more worn down Kuro's know it's all gonna come to an end, but at least it's better than lab life x3

Aww, I'm so glad to hear that I indirectly helped you by linking you to Incompetech :3 How did the presentation go in the end? I hope it turned out great and that you were happy with it :D

I would honestly love to say that your hypothesis on rainbows is correct, cos it sounds really awesome! But I'd be lying if I claimed that x3 haha. I hate to say it, but the rainbows don't really have any significance :( I wish they did now you've said what you said cos that would have been a cool idea to have! In truth though, I don't know why I picked those backgrounds >.< I had a big resource pack of free backgrounds that were all different colours with different patterns in and for some reason my brain decided to go with those ones to represent the transitions between simulation and reality x3 Since they don't have an official meaning, your rainbow theory could be adopted as canon if ya like :D Cos I think that's a really neat way of looking at it!

The rainbow places are supposed to kinda be like within her consciousness in between worlds, yeah, cos it's like there's no actual physical space when transitioning, so the only thing there is the mind :3 Kinda the same as some of the moving backgrounds like the goopy ones and the sparkly ones are supposed to represent the same thing.

There's no real reason in particular why Kuro was pulled out first in the princess route. It would have happened in other scenarios that we don't get to see as well, it's just more common for Isaac or Raine to allow them to have a sort of goodbye at the end. Though I guess you could kinda look at it as when they're allowed to have a nice goodbye together it's when Raine is overseeing operations since she's kinda, and when Kuro is pulled first it could be when Isaac is overseeing cos he's not as nice as Raine x3 haha. And yeah, the reason he usually helps her is because the transition is kinda jarring and would possibly leave an imprint in her mind of the change between worlds even after memory wiping. It's more that Kuro is ordered to send her to sleep that way cos they don't want her gaining too much awareness of the simulations. So if she's blacked out it's easier for them to move her mind from one place to another. Kinda like putting a computer into sleep mode x3

I'm sorry once again for how late my reply is! I hope you've had a fantastic week + that you have a lovely weekend :3