Hello Craig, we talked at Heart of Ohio.
Your problem could be a couple of things in my opinion;
1) The inductance from the long leads are inducing a back EMF* voltage problem for the MOSFET drive transistor located in your ECU from the highly inductive load (i.e. starter motor and leads). As the magnetic field collapses in the windings of the motor and leads it induces a high reverse voltage that is detrimental to the MOSFET.
2) As I do not know the part number of the MOSFET that is used I can only theorize that the Rds on resistance of the MOSFET may be too high and it is causing a localized over temperature of the MOSFET which in turn could cause it to burn out (i.e. too much power dissipation in the device and not enough heat sink). However this seems unlikely because this would have nothing to do with lead length of your setup and everyone would be complaining of ECU starter failures in normal (i.e. short lead) installations.
To solve for number 1 is easy if you are comfortable using a soldering iron.
You can install a Flywheel Diode to protect the MOSFET; ideally you would want the flywheel diode as close as possible to the device you are protecting; however, I’m sure you don’t want to try to stuff the diode in the ECU enclosure; therefore, I would install it as close as possible to the connector of the ECU.
You want the Cathode of the Shottky Diode connected to the most positive lead going to the starter motor and the anode connected to the most negative lead.
I would use a Shottky Diode that has forward current rating of 20 A (or more) and a reverse voltage rating of at least 15V, one suggestion is as follows:
http://search.digikey.com/scripts/Dk...PS20L15DPBF-ND
*
http://en.wikipedia.org/wiki/Back_EMF
Rich