Try extracting the files to My Documents and running ShopSim.exe.
.jar files are java's file package format. You run the entire .jar file, not any specific file inside it.
Just right click on the MyLittleSaveGameFixer-0.0.81.jar file and select Open With. Then select Java(TM) Platform SE Binary.
Here's a picture.
Instead of closing the entire game, you can enter sandbox mode, then enter shop mode again.
Right click it, select "Open With..." and select Java(TM) Platform SE Binary
Someone in the discord created a tool for that. It should delete all ores in your game.
http://mlbs.slipcor.net/
I've found I can minimize spillage of the open boxes with items inside by crouching first, then grabbing the crate. It's pretty consistent.