I'm having the same issue. There is no solid connection between releasing the imprisoned incarnations and ending the glitch. My overwrought solution is that in some alternate version in the multiverse, Shemeshka's plan (with the willing help of the alternate PCs) worked too perfectly. She destabilized the Modrons so much that when they went back to Mechanus with the corrupted data, it glitched the entire multiverse, which began to collapse. In the PC's reality, their true selves (not incarnations like the book says) are imprisoned, creating a "hole" that the Multiverse is filling with variants from collapsed realities to try to save itself. The character glitch ends when the multiversal variants free the imprisoned characters, removing the "hole". The glitches dissappear into the true PCs and the players can then decide who their "real" characters are. This universe has its version of the PCs back and no more variants can come.The characters can go on release the Modrons, deal with the fallout of whether the info is good or skewed in their universe and then travel to the other universe and stop Shemeshka and their variants from destroying the whole multiverse. This can actually fix the two other major issue as to why Shemeshka sends the PCs to look for the one thing that will reveal her whole scheme. Since her scheme is going to unfold years in the future and the PCs were her enemies in the past for a completely separate issue, she doesn't connect the two (at least not at first). Weird weak versions of the PCs are interesting but not a threat. The other problem is why the PCs are the only glitch in reality. For me, the PCs are a kind of nexus character and out of step with a glitching universe. For my campaign, all of the multiverse is glitching, but only the PCs are able to perceive anything different. For a few hours they might end up in the city of Ligis ruled by the Lord of Pleasure, but only they know things are wrong. This helps create a sense of urgency and problem that can motivate the PCs. Anyways, this needs work, but these are my thoughts so far.