Those questions aren't stupid at all.
1. The process to remove sulphur from the fuel has the side effect of reducing fuel lubricity. Some people are concerned about injection pumps and injectors wearing because of this. However, I think the refineries will address this issue with an additive since the last thing they want is to be accused of ruining all the diesel engines in the U.S. In Europe, where they've had low sulphur diesel for years, all the pump diesel actually contains 5% biodiesel, which provides the necessary lubrication. I run a 20% biodiesel mix right now, so don't have any worries.
2. Lil Pete is mechanically injected. Everything about that engine is mechanical once it's started. You could take the battery out of the car and it would keep humming along.
Edit: geeze, I guess I'm a slow typist. I started when there were no replies to Jen's questions.