By copying the Game.rgssad file over, you've effectively replaced the game's "brain" with the one from the last update. Nothing is gonna work.
Your save files transfer automatically - all you need to do is download the new version and launch Game.exe. You can delete the old folder as well. I do not recommend extracting the new version to the old folder. Just extract it somewhere else & let the game do the work.
Save data is stored in your PC's Roaming folder.