@alawiggle - looks to me like you are not on the right branch. Make sure you are using the 1300D branch:
cd ~/magic-lantern
hg update 1300D
cd minimal/hello-world
make MODEL=1300D
Next copy the autoexec.bin from the onto the QEMU sd card. I'm on a Mac so I just double click qemu-eos/sd.img, drag in autoexec.bin into the root directory, eject the virtual card and run it.
cd ~/qemu-eos
./run_canon_fw.sh 1300D,firmware="boot=1" -d debugmsg
@critix - I've been meaning to getting around to merging your pull requests for the 1300D and 4000D but want to come up with a strategy. What do you think, make a new 4000D branch or a new digic4+ branch? Just adding the 4000D code into the 1300D branch would probably be confusing.