Cranks but will not start

I have numerous relays in both fuse boxes that are damaged this happened after the main power wires from starter and alternator to battery fell onto EGR valve pipe melting a dip like hole into the metal of the pipe. After this the car would crank but not turn over so I changed my harness to the engine coil pack that melted changed the crankshaft position sensor and its harness plugs and wires all wires from alternator and starter to battery. Had alternator rebuilt and replaced starter. Then pulled out all relays both under the hood and dash and found them to be bad even though some lit up when using a test light. But when I push in on some relays under my hood one makes the headlights come on another makes the fan come on and another makes the chime noise sound inside the car. I checked the EECM and PCM they appear fine, but the screw that holds the harness into the computer has broken in half with half on each side of the harness the other half in the computer. Now my question is, would replacing the fuse boxes help at all? Also how can I get the broken bolt out of each part of the computer? Any suggestions on what else I can try or do you think it is a total loss on the car?