I finally managed to find time to assemble my Maker Shed Brain Machine Kit, and knocked it out today in spite of not having instructions until I finished. Since it is based on the Lady Ada MiniPOV3, this is a less difficult task than it sounds.
When my kit arrived I was confused by the lack of additional instructions beyond those linked from the product page above, which refers to Make Magazine Issue 10. This page provides firmware and schematics sufficient to build the device from bits and pieces, but I was looking for a cakewalk. I sent a message to tech support at maker shed and they suggested I look at "Hacking the Brain Machine", which turned out to contain a pretty decent picture of the completed device. I only had to figure out the audio portion, which was pretty straightforward given the schematic.
I was finally sent the instructions, but as they come in the form of the article from Make I am unsure if I should pass them along. The instructions above should give you enough information to build the kit; if not, drop me some mail...
Found online plans
Aha, the link to the free online version of the Brain Machine article: http://cdn.makezine.com/make/wp_brainmachine.pdf
...and Ubuntu instructions
Install
avrdude
andavr-libc
to get the tools you need (deps will be pulled in.)...aaaannnnnnnd annotated, updated instructions
Do-It-Yourself Projects by Mitch Altman, and friends.