If you want to keep the EEC grounding as Ford intended it, and trust me, as an EEC designer, I can attest that Ford did all this for good reason, run 40 and 60 back to the battery negative with separate 12 gauge wires. 40 and 60 are EEC's high current ground dumps, and they want to return to a good, low impedance ground, and it doesn't get any better than the battery - terminal.
Running important grounds through the chassis is asking for trouble. The chassis is highly inductive, the ground paths change as the vehicle moves and flexes, and it all gets worse as the chassis ages, corrosion builds up, spot welds break, etc.
EEC pin 20 is called "case ground" and is a noise dump. Each of the signals on the EEC 60-pin has a resistor-capacitor noise filter which is meant to filter incoming noise and bypass it to ground before it gets to the EEC internals, but Ford did not bypass these noise filters into the power ground (pins 40 and 60), rather, they (smartly...) bypassed the noise filters into pin 20, which is meant to dump noise into the vehicle chassis local to EEC. Keep the wire from pin 20 short and tied to the chassis.
Edit: I'm not saying that what you're doing won't work, plenty have not followed these guidelines and been fine, but if/when EEC starts doing wacky/unpredictable things, grounding it as the designers intended will often fix the problems.