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Instead of daisy chaining the relays for the main power like that, why not just use a transistor to switch the larger relay. I assume you did it that way because you didn't think the AVR output could drive the large relay directly. It's clunky the way it is.
I think you chose a device with a few too many IO pins, also. My first shutdown controller used a 12c508 (8 pin device), my next one (which includes a bunch of I/O and servo controllers) uses only a 16 pin device (16f88 IIRC). A 40 pin device is huge for such a simple task.
D2 is kinda redundant. I usually do reverse polarity protection by relying on the fuse popping when the zener forward conducts (or another diode in parallel). This just reduces the voltage drop before your circuit gets the juice (all kinda academic since you are using a linear regulator anyways).
You might want to put a pull down resistor on ignition sense too.
Relays are noisy for switching. A lot of power-switch-press circuits just ground out one of the power switch leads with an NPN transistor or FET. Much cleaner design that way, and less noisy, lower power, smaller, more reliable, etc... Similarly for the main power switch. Might I recommend a high side driver or FET.
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6yr old first install died 20/8/2005 as result of bad bios flash.
New system : 6x5x2" contains 1GHz C3 PCM9373, ISR based PSU, 512Mb flash DOM, 8Gb CF HDD, 98Lite, DirectShow based frontend.
GPS : Rikaline 6010.
Display : LTM08C351 + LVDS receiver.
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