There'd probably be a partner system, similar to IN, except they partnered up with their PC-98 counterparts. The teams would probably be Reimu/PC-98 Reimu, Marisa/PC-98 Marisa, Alice/PC-98 Alice, and Yuuka/PC-98 Yuuka. Sakuya would most likely be involved in the time travel part, but nobody would know who she was. Because of that, the final team would be Sakuya/Yumeko just because blade-wielding maids, lol.
Sakuya would probably be very confused, especially when youkai started trying to murder her, since the spellcard rules didn't exist back then. She'd ask Yumeko about it, who'd explain. Sakuya would then start
murdering defeating every opponent with ease after hearing that. Reimu and Marisa, on the other hand, would have to be veerrryyy careful with how they interact with the inhabitants (so as not to change
Touhou's canon the future of Gensokyo) Knowing Marisa, she'd probably try to steal the Five Magic Stones with her counterpart. Reimu would start showing off to PC-98 Reimu, because she could now fly all by herself. PC-98 Alice would be amazed by Alice's dolls, and would want her to teach her how to use them. Yuuka would visit Elly, and then she'd depart with PC-98 Yuuka to battle others. Of course the game would include the "dream meter" for old time's sake.
The final boss would probably be Mima, because she's jealous that the other player characters of the PC-98 era made it to windows, and she didn't. Of course though, everyone would be friends at the end, but would be sad to see the windows characters leave
Then Yukari would get upset, and yell at everyone for messing with the past.
What if Kogasa's umbrella got struck by lightning?