The two main options that I know of are (a) an aftercooler and (b) alternative engine management controllers. There are two basic aftercooler configurations; however, neither of which are really easy to work on.
Glenn - don't take this as an "arguement" but I think that minor changes such as headers or cold intake, can be compensated for with the factory ECU. This of course is predicated on the assumption that there has not been an AEM or Haltec or Motec that replaces the factory ECU.
Steve - if you would like to discuss further in detail, call me at 713-215-8016.
If I had to do it all over again, I like "sampson's" aftercooled CTSC.....very clean installation.