The 6L engines last a long time, you can put 100K miles on them and they'll still run good, all gen III engines can take 100K hard ass miles, so I guess if you find a badass deal on a complete 6L, i'd go that route. If you looking to tuffin it up a tad, go for the rebuild.
Yes, on the filter, procharger has a cone filter right on charger itself, not in the best location, right above the driver side manifold.

later,

allen