Your graphics look pretty good. I look forward to seeing the a game demo. Did you break all your sprite elements down to the size of your grid? Or do you all sprites to be a size factor of the grid size. i.e. sprite can take up 2x2 grids?
I'm not sure if I understand your question correctly, but I'll explain how i have implemented it. When you start a new project you can define the size of each tile in pixels. In the code I have left support for two different parameters, one size for the tile set, and one size for the map. But at the moment you can just choose a common size for both of them. I have tested this by hard coding different sizes and my solution for handling the different sizes is to, say that you have chosen 32x32 pixels for each tile from the tile set and the map has tiles of size 50x50. What happens is that the tiles from the tile set are stretched to match the size of the map. Does it make sense? The reason why I haven't added support for this is in the GUI is because i don't know how to handle this when I export the completed level. I will later on add support for placing characters on the map, and they will be separated from the tile system, making it possible for them to have bigger textures separated from the tile system.
I haven't made the tile set myselft, it's just something I got from the Internet, but we have people drawing tiles, so hopefully our finalized products will look good.
Why not use Tiled?
IIRC, there is even a link to the Java source.
(so you can have a look around at how it handles tile maps)
I'm aware of that. When I started I had no idea of how image manipulation and everything related to level editors works in java. So instead of studying the code and try to understand I thought that in the end I would save time by implementing and learning it all by myself. Now when I have an idea of how this works I'm thinking of starting to contribute to Tiled instead. I've implemented a file-parser for it for one of my projects in C++ and I think that their solution for the exported file looks much better than mine. I did this since they have support for isometric view and it wasn't anything I was planning implement for my own editor.
And it's a bit too late to look at their source of how to handle tiles, since I'm done with my own implementation of it, but I'm sure they're a bit more organized than my negligently implemented MVC-pattern.