>Progression
The thing is, I don't think that his natural progression and focus on mental recovery would be hampered. If anything, helping Matsui is close to the pinnacle of the "I want to take the entire world's burden even if it'll kill me" attitude that I want to have Valentine display.

I'm also not really sure what you mean by "different shenanigans." I never planned on him staying in one place or anything, and every chapter was supposed to be a new challenge, whether that be a physical threat by a Pokemon, or something that came within. Maybe I'm just missing the point though, and who the hell knows if I'll be able to even stick to that.

The planned outcome whether he got Matsui or not was always the same. Valentine goes back to road tripping, and eventually he gets too many Pokemon to carry in his sedan, so he goes ahead and buys an old recreational vehicle which he modifies to suit the needs of his companions. (Primarina was an example of "suits the needs" I'd been considering. He could install a big ass aquarium in the back, making sure the Primarina always can hang out in a wet environment, even if it doesn't really fit the Primarina's size.)

>chemistry
Matsui's lack of chemistry towards Valentine is largely because, well... She woke up as a Pokemon on the entirely wrong continent, and got into a fight with her family/boyfriend/best friend/whatever(haven't really thought about it too much beyond it being someone she'd be distraught over) over the situation when she called for help. 

Not only is she now a quadruped with no phone, no identification proving who she actually is, left with a bad social situation she can't exactly resolve easily, and no currency to work with, she's also battling thoughts scratching at her mind, telling her to act a specific, inhuman way-and she idly complies whenever she lets her guard down. As if that wasn't enough, to add ON TOP OF THAT, she has to rely on foreigner hospitality in her dark hours, while battling the sense that it's rude to do so and finding out it's exceedingly rare to find people who speak enough Japanese to actually help her. Her limited English doesn't exactly help things either.

I feel like very few people would be able to resist becoming incredibly bitter over that situation. She's afraid and lashing out. Her actions are of that of a woman who's trying to find any semblance of control over her life right now after having practically everything stripped away in the blink of an eye.

I have a chance to have Valentine help her, and have her warm up as a result. That was, after all, my original plan. Her realizing that Valentine's not just some fleeting help that will disappear as soon as it's no longer convenient, but someone willing to help her through thick and thin, even at the active detriment to himself. I dunno, there was room for growth and healing for both of them in this, was what I was trying to say.

>so what's the problem?
The fact I don't have any way to reunite Matsui in a remotely good way. I wrote myself into a hole here. Matsui's stuck in California, which, despite the fact Valentine feels some nostalgia for, he doesn't really want to return to either. Matsui's also pretty certain on returning to Japan right now, because that's where she LIVES. Everything she's ever KNOWN is there. Even if he came back, why would she bother with him when she's so narrowly focused on just going home?

The original plan here was an LA insurrection. ICE and the CDC would team up to try to send those who got teleported home. There's an ICE facility in Los Angeles. However, Matsui doesn't have ANY proof of documentation, so they'd need to rely on Valentine to confirm her identity and provide his own proof(the phone call to Japan and the fact he knew her name before reading the news article would be enough, at least for plot purposes.) 
From there, all I'd need to do is have some people who just hate America try to decide to take advantage of the chaos and politically charged environment, try to frame the United States as a weak colonizer or whatever, and since Valentine was there to confirm Matsui's nationality, the duo escape the chaos. This has the effect of Matsui generalizing that it's too dangerous for her to try to use ICE to return because... well, she just got fucking attacked in a government facility by some very, very angry people.
It also has room to introduce other concepts, like the Arcanine and Hisuian Zoroark. Valentine being involved there probably would piss SOMEONE off enough for revenge, and those characters could be manipulated to try to kill him. Far more interesting shit than the time Obama almost killed Valentine, I assure you :P
As I said, the whole thing is gratituous, and the aftermath of such an event would be ridiculous, which is why I've pretty much put the idea in the ground, even though I'm not talking like I have done so.

I did think of something very, very interesting while writing all of this though. Matsui could return to Japan, and then Valentine, for whatever reason, could visit Japan for a bit. That could lead to a reuniting. I can't see Matsui staying with him permanently though, unless I make Matsui's life pretty miserable in Japan too, which doesn't... really make me feel happy about doing.
Really wanting to have my cake and eat it with this story.