How can I make a custom document that becomes the default document.

In the templates directory there is a file called default.svg, which you can change to your preferences .

Recommended reading:

• Alexandre Prokoudine's great article “Using templates in Inkscape” (Libre Graphics World)

I'm just about to write a quick little tutorial, so I'll post in Tricks and Tuts subforum, when I'm finished. But the article recommended by ~suv should tell you everything you need to know