I can take care of it, yeah; I haven't had time to update the script from the last version yet, but I don't think it will actually be necessary.
Now, this game is pretty stable regarding randomness: there are very few things* that use the actual RNG, most using instead the in-level frame counter or the v-int counter. I would say that the safest option would be to edit each zone before moving on to the next zone but, except for the animal patterns, I can see very little odds of things going wrong before Final zone.
Just a question -- since you mentioned a "no zip" run, I would guess that would entail not zipping in Green Hill zone 2 (or risk the run being rejected for failing to adhere to its own goals). You will be doing that? (and yes, I know that deciding whether or not to use zips is a pain; I have been there...)
Also: I imagine you plan on hex-editing the end-of-acts later?
*: Specifically, the lava balls created by the Marble zone boss, the plasma balls in the Final zone boss, something else I can't identify in the Final Zone boss, the animal and explosion patterns in capsules, the animals freed from badniks, boss explosions, bubble movement and generation and the drowning countdown.
Edit: As if to prove my point, when I spliced the better animal pattern, Marble zone 2 desynched. I still have to look into why, as I simply copied/pasted both Marble zone levels with my resyncher script (which, to be fair, only handles differences in lag).
Edit 2: the difference was at the bat at around 6:00 -- he is too far forward and causes slight differences in subpixel position that propagate. By about 8:00, Sonic is half a pixel further left (and with a different subpixel y position as well) compared to the last WIP you posted.
Here is the spliced movie (with all input past the point of desynch still left).
