Liz… I had similar problems when I got to that point in the build. Though I can't give you a quick solution, here are some tips I have gleaned from the process (don't take offense if some of this seems obvious):
Make sure when bootloading (I used the USBtinyISP as well) you use the power jumper on the tinyISP. No external power is necessary (that goes for the extruder board and the motherboard). It turns out my first motherboard had some soldering issues; I ended up replacing it. Definitely check for bridges/orientation mistakes/etc.
You can't really test the stepper boards until the motherboard is bootloaded/working. The stepper drivers themselves aren't programmed, they are only used to communicate with the motors. There is a program (linked to at the bottom of the stepper driver build instructions) which you can load on the motherboard to test the driver boards.
The only way I can think to troubleshoot the tinyISP is to bootload something else with it. I have a few arduinos lying around, which is what I would use.
