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While we are on the subject of how harsh this environment is for electronics may I suggest LM2940T-5.0 as a replacement voltage regulator with the proper filtering. I too also agree with opto's maybe 4n35 or at the very least a transistors on the input. 3 or 4 bucks extra will go a long way in possibly saving to replace Atmega etc, just my 3.26 cents
http://www.national.com/ds/LM/LM2940.pdf
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A nice choice, what with data sheet info saying this is specifically for "vehicular" environments, and that it has overvoltage shutdown in case of higher voltage spikes. It can withstand 60 volt spikes in certain versions. I don't say this is definately better, but I would be tempted to use the 9 volt version, and use that to feed the 5 v regulator already on the board (or at least on the decimellia I got). That way we would share the thermal load of the voltage drop between the two regulators. Might get away without a heatsink.