Hey dad,
My truck is the same as yours (2000 6spd) and had to change it.
The crank sensor is on the lower left-side of the engine, behind the starter, and is held in by one bolt-down clamp. You'll have to remove the starter to get at it. The sensor cost $40 bucks from Cummins.
If all you have is an Edge box, I'd say remove the box and take the truck to the dealer anyway... they're not going to know you had it. Even if they did some how find it and deny warranty, what good was the warranty anyway? It's neither good now nor later on.