What would happen regarding the Gary Stu? Would he be one of the Sue Lord's regenerations, or a second Suvian character entirely? Because if he's not part of the regeneration cycle, what would happen to him in-between chapters? Nah, he's probably just one of the regenerations. It makes more sense that way.
I've been working on a vaguely formatted fic-dimensional idea that says that basically, if an individual Sue is killed, but her influence isn't expunged yet, the badfic defaults to the next state it's in when the Sue is not present, retaining the damage until it can be removed.
Expanding on that with insertion of the Sue Lord idea, the PPC would have accidentally contributed to Suvian natural selection by hunting down and killing the most obvious ones. In most cases, such as in the Pit, this results in slyer and/or less readily obvious Sues, but in undisturbed areas like the Circle, the native Sues use the badfic's shift to points in time where an individual Suvian presence no longer exists to regrow into new forms, not part of the same presence but working for its goals, to be capable of surviving to warp the canon for a longer period of time. Thus, the Sue Lord is created, through time-space distortion and Suvian stubbornness. When a Sue of this breed is captured, killed, or otherwise removed from the events of her story, the massive glitter index would force the creation of a new Sue from the warped Word World, or the corpse of the first if it was available.
Where Time Lord regeneration compounds the memories and experiences of a Time Lord with the new personality to provide new and improved experiences in the future, the Suvian Regeneration would take the parasitic tendencies of Sues to their logical extreme, as the future Suvian incarnations actually feed on the glittery bodies or canonical shambles of their past selves to rebuild another Sue to continue where the last left off.
This is where my Timecop idea would have come in. Since you seem to have planned to write this with DawnFire alone, I suppose I'd have nothing to lose by at least saying my idea here.
In the Timecop continuum, due to wonky time principles and the screenwriters not really knowing how to write a time travel movie, the "you're not allowed to interact with future or alternate versions of yourself" principle that time travel media enjoy is taken to a titanic extreme. When a past self makes physical contact with a future self within the Timecop continuum, both versions melt together in a slimy pile of ooze, which slowly shrinks as the time-displaced matter cancels itself out, and anything that the past self would have done from that point until it becomes its future self is removed from space-time. It's really weird, but that's what the movie claims, and that volatile time-reaction is eventually used to defeat a central antagonist.
I was thinking that if most of the Sue Lord's forms are captured rather than killed, they could be brought out of the continuum and executed in Timecop's, which would not only make for easy cleanup as they delete each other, but it would also make for a semi-poetic death when the Sues that mess with Time and Time Lords are killed by another type of messed-up time paradigm. You'd need to remove the "arch" reactor from the chest of the Torchwood Sue before this happens and somehow keep Jacques Bonnifoy(I like his new name, too) from being removed by reassertion of the timeline, but I think it'd be a pretty decent method of disposal at least, and as for keeping Jacques alive, well, PPC Agents are usually quite good at improvisation.
I'm not even sure what it's a monument to, but it's a pretty versatile arch shape, which is why I decided on it as opposed to a thicker, blocker arch shape like 
