We installed a 3.8 super charged engine in a 2001 Pontiac Boneville.  The car went about 200 miles and 1 piston is scuffed and all of the pistons look burned on the tops.  The engine was exploded when it came in so we changed the mass air flow sensor as a recaution before we istalled the engi.  We also installed a new intake manifold.  Any information would be appreciated.

Not sure i can help you with your problem, but i can maybe point you in the right direction to find your answer. The 3.8 had many iterations so you should check out the article by Doug Anderson on identifying the parts and rebuilding tips... e.g, there have been five different pistons used since 1988.

http://www.enginebuildermag.com/Article/4142/rebuilding_the_38l_buick_engine.aspx

Good luck,

Brendan