I've been working on reverse engineering parts of the Chrono Trigger PC build on and off for about a year using IDA Pro. It is actually a direct port of the SNES version. It appears that Square Enix wrote a lifter for 65C816 assembly that outputs C++ and then built off of the output of that, refactoring as much of the lifted codebase as they could. Some portions of the engine are straight C++; other parts are a mess of bit ops. I recently learned that the Android version was accidentally linked with partial debug information, so I've been referencing that to annotate more of the code. Initially I worked off of Geiger's notes and they helped me discover and annotate the field map script interpreter and the battle script interpreter.
I've successfully hooked the game with a proxy directinput dll and overridden some scripting functions in my early experiments (about a year ago?). I've been doing this alone for a while now. I'm trying to find others with reverse engineering experience who would like to help/take over the project. My intention is to slowly rip out parts of the engine via hooking into a seperate DLL until I have a recompilable codebase for the Chrono Trigger engine. If anyone would like to help please message me on this forum. Experience with the original SNES CT engine would be awesome too since large portions of the original game logic are still the lifted SNES assembly.
My current IDA Pro database for the Win32 version can be downloaded here: https://www.dropbox.com/s/2scov0yezhlsdcn/Chrono%20Trigger.idb?dl=0