Hi Keith,
Must confess, I was wondering about relays...
What else could possibly have got damaged by the short though? There can't be that many candidates. I bet it's something really simple.
Have I understood how it works correctly in that the coil packs receive a modulated signal causing them to spark appropriately? A short somewhere holding the pack inputs at 12V would explain the symptoms wouldn't it? If so, could we try bridging the connection to the coil packs from wherever the modulated signal comes from? Are both packs fed from a common source? Seems odd that they're both not working.
Or is that all just gibberish?