I think you made a big mistake. Your considering a supercharger? By the time it is said and done, you have voided your warranty, most likely will have tuning issues, later on blow your engine due to a bad tune (happens all the time) and then before the blown motor will have spent more than what the deisel would have cost. Even so if all went well intially, that motor wont last long becuase it wasnt setup for blown application with forged internals it will live a short life with the towing. Leave the truck oalone or cut your losses and learn your fromyour mistake. Should have gone deisel from the beginning bud. Sorry to piss on your parade but you should have did more research before your buy. I have an extensive history with doing blown and turbo applications in mustangs so just wanted to let you know, its not something that you do once and all will be good and dandy for the next couple years.
Also, gears are the only thing that will make a difference. intake and exhaust will not make any seat of the pants gains. only gains on the dyno but minescule. A programmer wont make anything noticeable either. Programmers will only make huge gains on deisel applications