Hi Kendall,
I used to do a lot of stuff with micros. AVR is a favorite. Here would be my suggestions.
Stick with the pre-made teensy-2.0++ or something like it - I believe the AVR you mention does not have a USB peripheral, while the one on teensy2.0++ does. And while there are software to bit-bang USB, this is very limited, slow. Unless you are planning to produce 100's of these, it's probably not going to save you anything to try to make your own board. These little modules are built with socket pin IO, so they already are extensible.
A lot of it is up to the software as well - even if you have the USB peripheral, they are quite complex, and having someone elses MIDI project with a pre-configured MIDI HID as a starting point is going to be very helpful. So go find a few existing AVR USB MIDI open projects, see what AVR micro they use, try to re-use them.
So what do you do with the shift registers? Do you mean like real shift registers? Or are they a software construct?
ATMEGA328P send MIDI via USB
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