OK. I managed to give it a try and found out I missed the Sonic save at GameFAQs is a Wii save. That explains why it is so big and got wrong at suggesting such save for a Genesis FRAM sonic3u.nv file.
I also found out there exists an online save file editor for Sonic 3 and Sonic 3 plugged to Sonic and Knuckles. However I could not have enough time to test it properly. My attemps failed at making it work with MAME. You could try it maybe.