I'm trying to transfer my save file from FC that I completed on steam to SC that I bought on GOG. The save file I'm trying to transfer is at the end of the game when it asks you to save clear data. I saved it at that point, watched the ending cut scene, then closed to game.

I opened up SC, and the config tool showed me the save folder location, in my case it is C:\Users\Josh\Saved Games\FALCOM\ED_SORA2

I copied and pasted my entire save folder location from the steam version of FC located at C:\Users\Josh\Saved Games\FALCOM\ED6

I then started the GOG SC version, and went to load, and nothing showed up. (EDIT: I also tried Start new game and did not receive a prompt asking me if I want to use my clear data like other guides said it would). Every guide I've looked at says to simply put your save file in the folder that SC looks for and then it should show up and you should be able to load the save file(EDIT: not load, start a new game with a prompt). Instead I can only start a new game (Edit: Without a prompt acknowledging my saved game).

Am I doing something wrong? I would really like to have the decisions and quests and such I did in FC be carried over to SC. I even tried using a save file that someone else posted in a steam forum. Nothing's working!

Then every guide is right, you are just reading it wrong. Put it in the folder that SC looks for. SC looks into FC save folder, when you are trying to import FC clear save. It's designed to work without copying anything - at least I didn't have to.

I can at least confirm that you have the folders right. On my computer (win7) the folders in GOG version of both games are:
FC - "c:\Users\<username>\Saved Games\FALCOM\ED6"
SC - "c:\Users\<username>\Saved Games\FALCOM\ED6_SORA2"

In other words, GOG SC should be able to load Steam FC clearsaves, no copying required. Did you by chance do CUT & paste, instead of copy? If you start FC, can you see your saves?

Just a sidenote: no decisions or quests are carried over, as far as I know. If you have Estelle over (45?) in FC, she starts at 40 in SC, otherwise she starts lower. And if you have perfect FC game (all BP), you will get some unique quartz near start of the game. Other changes are just cosmetic (you could read through your junior bracer notebook if you import).

I did not cut, I copied. I can still load up FC and my save will be there perfectly functioning. I do not understand why this is refusing to work for me. When I check the Falcom folder ED6_SORA2 and ED_SORA2 are both there, I've tried putting my save file in every single folder juuuust in case the program is looking at other folders, and nothing happened. I've tried having the save file only present in only one folder at a time, and nothing happened. The game refuses to acknowledge that I've beaten the first game =/

FC saves should be under the %AppData%\Roaming\FALCOM\ED6 folder. SC switched to c:\Users\USERNAME\Saved Games\FALCOM\ED_SORA2.

I don't have any FALCOM directory under either Roaming or Local and still can load and import my FC saves. But there WAS some confusion with save location in FC, way back. I remember "losing" my save games after one FC update, until I moved them to where they are now (it was more ancient version than Galaxy rollback allows). It's worth a try.