Being a 2004, you cannot do EFILive or H&S (2006 and newer can but use a different computer).
You are limited to all the others; Smarty, Edge, Banks, Bully Dog, and a bunch of others. Notice that I have listed Smarty and Edge first.
The Smarty hand-held is going to be your best bet for tuning and power. You can manipulate multiple variables to 'fine' tune your truck to match your current mods (none) or any mods you add in the future. You can add power without getting wild EGTs. There is an issue with the Smarty's causing the Grid Heater light to come on, and I don't remember much about what the cause/solution was. Along with the Smarty you get UDC tuning (do a web search for it). It is the next best thing to getting EFILive (that isn't available with the 2005 and older CR Cummins).
I have the Edge Juice with CTS controller. Plug and play. No jacking around with tuning/testing since it has already been done. A tap with the finger allows an increase of power on the fly. Has a built in boost fooler (~37psi). The downside with the Juice module is it runs hot; all the tunes are hot. EGTs definitely need to be watched. A nice thing about the Juice is that with the Attitude/CS/CTS gauge displays is that you can set limits for boost and EGT so that the unit automatically defuels (to stock) as you approach the limit that you set! On my CTS I have multiple alarms set (high boost, high EGTs, High engine and trans temp, high fuel rail pressure) so that I don't have to 'watch' my gauges on every hard pull. It beeps and flashes and turns red the parameter that has exceeded (or fallen below) my set point. Really nice feature. Plus, the CTS will accept a backup camera! On top of that, you can get a turbo timer (shut off based on EGTs or by time).
If my truck didn't already have the Edge/CTS when I bought it, I would have went with the Smarty with a standalone CTS for gauges.
With mild tunes, keep the stock exhaust. It is 4" and many are running 500hp+ with the stock pipe.