Up till '94 they used the 7.3 IDI, non turbo engine in the E-series.
In '95 thiey switched to the 7.3 Powerstroke engine. It is a turbocharged non-intercooled engine that is virtually identical to the truck version. Tuning differences, slightly different intake runners, oil cooler, exhaust manifolds, non-wastegated turbo, but nearly identical.
In 2004 they started using the 6.0. This too is much the same as the trucks, but with a smaller intercooler than the trucks, different tuning. It delivers 235HP instead of 320HP. Ford is still using this engine, and doesn't look like they going to stop any time before at least 2010.
Ford will not be putting the 6.4l in the E-series van. It is simply too big to fit.