Hi AKEric,
There's not yet a way to view/edit the tool library other than when loading or saving tool definitions from/to it, but adding in a simple sort by type/size shouldn't be too hard. You can remove a tool from your project by setting its type to "None" under its parameters and hitting Apply. I'll go ahead and spiff up the tool library a bit and add a button to simply delete a tool. It's important to make sure the tool isn't being used by an operation still when it is deleted (i.e. change the operation to use a different tool and re-generate its toolpath before removing the previous tool it used).
Feel free to share any other thoughts/ideas/suggestions you have and I'm glad to hear PixelCNC is a good fit for your work :)
Charlie