You also might take a look at adding ferrite chokes to the wires as close to the unit as possible the right ferrite choke will strongly attenuate high frequency spikes on the wires.
you can also use shielded wire like RG58 coax for data lines that need to pass near the ignition.
https://en.wikipedia.org/wiki/Ferrite_beadhttp://k0bg.com/rfi.html <-amateur radio view of the issue, you might ask around the local ham radio groups to see who the local RFI guru is they work with this stuff all the time.
http://www.amazon.com/Handbook-Practical-Cures-Frequency-Interference/dp/0872596834/ref=sr_1_1?s=books&ie=UTF8&qid=1406486089&sr=1-1&keywords=rfi+handbook1967-1974 corvettes had shielded ignition wires as I recall, you might talk to your local Chevy parts supplier to see if any of their ignition wire kits can be adapted to your system.
Accessory spark plug resistor caps and special low emissions wires are available
http://www.magnecor.com/magnecor1/main.htm (checkout their faq THE TRUTH ABOUT IGNITION WIRE CONDUCTORS)
Polyphaser is one of the leading manufacturers of surge protection devices and they have a whole line of protectors intended to suppress spikes and transients on data line.
http://www.smithspower.com/brands/polyphaser/products/data-line-surge-protectionhttp://www.smithspower.com/brands/polyphaser/services/media-library/white-papersDon't forget your surges can be coming into the equipment on the dc power supply line, that can be clamped with a combination of MOV's and ferrite beads along with shielding of the line so it won't pickup the surge in the first place.
http://www.smithspower.com/SiteMedia/SiteResources/WhitePapersandTechnicalNotes/1457-001.pdf?ext=.pdfIt is a very complex subject and it often has to be solved by experienced trial and error elimination of possible paths for the transient and figuring out an effective filter to suppress the surge in that specific configuration, a solution that works on one car might be totally useless on another due to differences in the surge path or method of induction of the surge into the wiring.
Rules of thumb
Place high voltage ignition wires as far as possible from other wires (especially data wires)
If the ignition wires must pass close to another wire bundle put metallic shielding around the wire you want to protect and if possible arrange the wires so that the ignition wire is as near as possible at 90 degrees to the other wire to minimize the electrical coupling between them.
Assume you are getting spikes on you DC power supply and put filter components right next to the data system you are trying to protect with high efficiency grounding (not some slender little wire but a proper braided ground strap to a substantial ground) I would start with a MOV and transorb protector if you can find a data line protector that is compatible with your system wiring. (ie the right end connectors if you are using RJ45 data lines or coax lines to pass your signals)
Distance is your friend keep low voltage sensitive lines as far as possible from high voltage systems and if possible shielded by metallic shields that cover the wiring (or place on the other side of a fender panel etc. so a grounded metal sheet is between the two)
There are two types of coupling for high voltage surges, electrical and magnetic. A low conductivity shielding like copper or aluminum works best for electrical RFI, a steel or other magnetic material is best to shield against magnetic coupling. Best protection is a little of both a steel tube covered with aluminum foil for example to pass the wire through, and well grounded.
Use single point grounds if you can so that all electrical equipment is grounded near the same location on the chassis.