I have set up the check engine light in the dash but don't know how to check codes...how do I check codes?? It was black smoke (yes fuel?).

Fairly happy I have checked the basics... I have the plugs out and have spark at each plug..

The silver box (if you mean the ignition module) has been replaced. I'm wondering how the other sensors effect idling and running i.e. maf, map, tps, and the other one at the throttle body???