Here is the little app that will let you edit the shortcuts on the Vanilla Rainmeter Skin more easily. To use just pick a name, the location to your app (you can also use files and websites), pick an image for the icon, and where the icon should be on the launcher, and your done! The position numbering goes from left to right. You will have to refresh the rainmeter skin to see changes.
Hopefully this will make the Rainmeter skin more usable, but there's more to come!