Are you saying that you have spark with the wires disconnected from the ignition modules. With the factory smoke coming out of the wiring, you could of melted some wires together in the harness and causing a partial ground for the ignition modules,
You may need to open the harness up and check for cooked wires. And figure out what wires go where so you can hook the wires up correctly to the key switch. You may also need to replace the key switch to get the correct internal circuit to get it to work correctly.
