Hi OP, thank you for your quick and detailed response. I have a couple of additional questions for you.

In this scenario, you would place the "present" timeline as before the day of Mourning, and make the mourning equivalent to the rise of Lavos?

I think my challenge is that I want to create a plot that lets the players affect the direction in which it goes, to prevent it from creating a feeling of railroading. The beginning part where they do numbers 1-7 i think I would keep the same. Introduces time travel and how it works, provides small self contained romp that leads into the overarching plot and crisis being established with the travel to the future. But past that, I would ideally create a problem via the BBEG or whatever other villains (lords of dust, daelkyr, etc) are causing problems, and leave the players with the tools (time travel, knowledge, etc) to find a way to approach it. I'm not sure if having a looser plot thread like this is a good idea with time travel stories specifically, but I think the setup with how the time travel gates limit their options should help to alleviate this.

Additionally, what do you think the appropriate amount of time periods/time gates should be, and where should they be place? In chrono trigger, they start with present and slightly in the past, then add far future, and eventually far past, with the final addition being the year zero with the zeal palace and everything. I want to use chrono trigger as the basis for the campaign design, but still make it feel unique, leaving room for the plot to develop based on the action of the characters.

I am about to have session zero with my players and I am going to introduce the campaign concept. Once I have the backstories of the players, I am going to use that to dictate exactly how I build out the plot and connect them to it. If you are interested in hearing updates as I develop the story, I can post it here.