This can be done in the "new game" section using the code from the part of Window_SaveFile where it temporarily loads the savefile to show it in the Load File window. It also loads the game switches into @game_switches (not $game_switches).
In the "New Game" section, use Marshal.load to load everything up to the game_switches into temporary instance variables, then after $game_switches get initialized, set those specific switches to the values in your @game_switches that you read from the save file.
Why did I explain this instead of just doing it? My VX Trial ran out yesterday, and I haven't bothered to buy it yet.
So, if another scripter wants to tackle it, it gives them a head start...
Sorry I couldn't be more help this time.
Be Well