Hopefully I can find some good info in your post here.
The save files that were uploaded to Steam via Cloud Saves are intact and they have mod information saved in to them but I haven't figured out how to read that info yet. I am in the same boat as you as of recently having accidentally erased all of my Fallout 4 mods and settings and I have no idea where to start or exactly which mods I even had in the first place but there is hope.