Minecraft – My normal guiscale is the same as large & auto

I suggest you don't even use world edit, Making a bukkit plugin from scratch is very easy and very fun.

Bukkit's API has very usful block-editing tools, this peice of code here will place a block of stone(b.setTypeId(1);) above every player's head whenever they move.

    public void onPlayerMove(PlayerMoveEvent evt) {

    Location loc = evt.getPlayer().getLocation();

    World w = loc.getWorld();

    loc.setY(loc.getY()-1);
    Block b = w.getBlockAt(loc);
    if(!b.isEmpty())
    {
    b.setTypeId(1);
    }}

And as for the anti-crashing, just make the plugin run on a separate thread from the main server, this way if your plugin "crashes" the server won't respond any diffrently until the plugin has finished calculating and will finish at quicker speed.

In all tests simply putting my Minecraft window to fullscreen and then changing the GUI mode in the options allows me to have large buttons and font with a fullscreen minecraft.

I have tried both older and the most updated stable released version of minecraft. (no snapshots)

If this does not work for you for some reason my assumption would be your either doing it wrong unawares, or there is something wrong with your files.