You can buy the coils from Nology for about $75 each.
http://www.nology.com/profire.php or this distributor was very helpful
http://fasteddysports.com/
You want item No. 152 001 070. Alternately, Item No. 152 001 070T is the same coil but with Lucas/Triumph output connectors. You can buy the Lucas terminals on ebay and put them on the spark plug wires but Nology can also supply spark plug tower adapters that makes the Lucas outputs into sparkplug towers. You need .6 ohm coils for electronic ignitions. They are all made by PVL with a Nology label pasted on.
I would imagine that the cut wires to the crank sensor can be spliced or replaced. You can make new D-sub connectors with wires for the boxes. Klaus's manuals are downloadable on his website.
Lightspeed will checkout the boxes on request. He would probably redo the wiring for a price.