I like to think that the PC-98 characters are actually still around in the Windows era. One of my headcanons is that Ellen's Magic Shop is still there next to the Hakurei Shrine (after Ellen desperately begged Yukari to have her keep the shop there) and thus bothers Reimu on a daily basis along with Marisa. Next to no humans travel to the Hakurei Shrine though so Ellen mainly does business with the supernatural beings who come to mess around at the shrine (?).
Shingyoku still dwells at the Hakurei Shrine, which really annoys Reimu. They have a sort of a rivalry with Aunn as the protectors of the shrine.
Yumemi and Chiyuri were actually lecturers at the university where Renko and Maribel are studying at. It is mentioned in both the prologue for Touhou Yumejikuu and in the Magical Astronomy CD that gravity has been integrated into the main Unified Theory in the Outside World, so there could be some canonicity to it (?)
Rika and Rikako are close friends with each other, and live near the Youkai Mountain so that they can interact more with the kappas.
A bit off-topic but Sariel and Shinki are definitely related in some way. If Shinki is the creator of Makai, then could it be possible that Sariel is an accidental byproduct related to Shinki brought to existence during the creation of Makai?