"Prometheus" is not a code name.In a story like this, it does not seem at all unreasonable for Ancient Astronauts to exist. The Propmetheus in Conduit is the same Prometheus who taught humans how to make fire in Greek mythology.
Michael Ford is the Master Chief's great grandfather.The ease with which he gets used to wearing a cybernetic suit, his trust of talking metal balls, and his sheer badassery are all genetic. Unfortunately, so is the debilitating birth defect that results in him only being able to carry two guns at a time.
Prometheus's people are Daedra.Compare how similar in appearance and function Conduits are to Oblivion Gates.
Prometheus's people are Marro.The Marro have a type of unit that is actually called "Marro Drudge." They also look quite like the Drudge from Conduit, and utilize organic technology. What's more, the Drudge egg sacks function almost itdentically to the Marro Hive (spurting out low-level mooks to replace fallen ones), but on a smaller scale.
Ford is putting on a fake voice.This is why he sounds forced at times, and why the grunts he makes when he jumps sounds completely different from his poor-man's-Solid Snake speaking voice.