Hi, A lot of work has been done on this issue with all the electronics in today cars. Here are a couple of good resources:
Texas Instruments: http://www.ti.com/lit/an/snva681/snva681.pdf
A major problem may be "Load Dump" WikiPedia:
Here's an informative graph showing the challenges in the automotive "12V sort of" environment:
You really need some high-voltage transient suppression! The MegaSquirt is a serious approach to this. Overkill in combat with Bad Stuff that could happen and kill your Fuel Injection system at midnight on Route 95 in New Jersey is not a bad idea.
Good News is that this is such a common problem there are some good solutions. Texas Instruments has a nice voltage regulator, the LM2940 which is available in different output voltages. I would pick 9V output to run to the external power jack on an Arduino. Ti has done some work on the Automotive issue in the 2940:
Designed also for vehicular applications, the LM2940-
N/LM2940C and all regulated circuitry are protected
from reverse battery installations or 2-battery jumps.
During line transients, such as load dump when the
input voltage can momentarily exceed the specified
maximum operating voltage, the regulator will
automatically shut down to protect both the internal
circuits and the load. The LM2940/LM2940C cannot
be harmed by temporary mirror-image insertion.
Familiar regulator features such as short circuit and
thermal overload protection are also provided.
The DataSheet:
The part number for 9V and TO220 package: LM2940T-9.0 NS TO-220
So I would start with a little simple protection plus the LM2940 which should be available for about a dollar.
I'll try to go over that MegaSquirt schematic in some more detail soon...