Okay, so a lot has happened since my last project update:
1) Integrated the TrinketPro into the project. I needed to change my sketch a bit, but the big issue was that with the TrinketPro the power circuit no longer works. I just couldn't find a resistance level that would keep the processor off normally, but allow the transistor to keep it on.
2) Redesigned the power circuit. Some web poking and a post on the Arduino forums helped solve this issue. Solution was to utilize a p-channel MOSFET along with an n-channel MOSFET, using this as the inspiration:
3) Added a battery power monitor circuit and sketch. I use a voltage divider (two equal resistors) to bring the voltage below 5v, and then use an analog in pin to measure the voltage (x2 to get the actual voltage). Crude, but functional, and really it is just a low battery warning.
4) Added some UX elements to the sketch (e.g. when it is armed, can enter the code to shut it off without triggering the alarm).
The completed circuit is below, as is a video of it in action.
From the top:
And a close up:
A video of it in action: