I had something similar (cost wise that is) with me back in 2000, basically, after my black U12 had been broken into, i had some more stuff done with the alarm, when the car was done it would crank and wouldn't start. Alarm guy wouldn't take responsibility, what had happened was, when he was running another wire through the firewall, he ran the bloody thing through the same bloody hole as the main ECU harness, and what had happened was the shielded wire going to the power transistor (which fires the ignition coil) broke down.
The outer shielding (which is wired to body ground) was then touching the main conductor, so the power transistor wasn't getting a clean signal.
Ended up costing about $700 to fix, which was running a new shielded wire for the power transistor to the ecu, worst thing was, i had to source the fucking wire for the auto elec doing the job! Never, ever went back to either place, car never ran the same since that happened.
Needless to say, i plan on making a brand new harness for my black U12.