Good looking truck but lets start at the beginning and address a few things. I'm going to stress some things that will be vital to the health of your engine/trans/wallet, you may not like my advise but take it from some one who has been there and done that with a tuned/deleted 6.0. Your expecting a new child, your about to have a good amount of new expenses, are you sure that your ready to risk a $4k transmission and a $3-5k+ head job(minimum) by loading up tunes and going balls to the wall? I've been where you are (minus the child) and I can tell you that this is a long and expensive road your about to embark on.. BUT if your good with it and open to listening, lets roll...
Throw that Banks 6 gun in the trash. It will ruin your transmission. The SCT tuners (the tunes I run anyway) program the transmission AND the engine. They will alter shift points, and shift pressure to TRY to keep your trans in check and try to keep your clutches from frying. The Banks system only tunes the engine. These transmissions are notorious for burning out the direct clutches that control the 3-5 shift when they are tuned. You can buy upgraded direct clutch solenoids to help increase shift pressure but in my experience it was only a band aid.
I'm going to ASSume that you got the truck from a dealer so you don't know about the history or whats been done to it. The first thing you need to do is to get a monitor and/or gauges to keep an eye on the engine vitals or at least have someone with a scan tool (Auto Enginuity or Snap-on, etc) check your vitals to see what she looks like. I use Auto Enginuity for trouble shooting and an Edge CTS to monitor vitals (there may be better monitors now, i've been out of it for a little bit).
Judging by the engine pic you posted, I believe you have a stock oil cooler (the lack of additional braided hoses coming from the top of the engine is a giveway). Looks like they changed one charge pipe and the intake pipe and intake elbow (looks like stock intercooler boot on the turbo). Unless your going for BIG power, the factory intake/filter setup is perfectly fine up to around 600hp IIRC. You won't get 500+ unless you do bigger turbo and injectors. The pretty stuff is just bling, aside from maybe a couple threaded bungs in the intake elbow your not gaining much of anything over stock (plastic charge pipe is still there as well which i'v seen crack and leak). I'm curious to see the studs your referring to as well, that one pic looks like a factory TTY bolt. The studs will have 12 point nuts on them.
What are your oil/coolant deltas? Temp difference between the oil and coolant need to be under 15* (they may even recommend below 10* now), if they are at 15* or higher your oil cooler is starting to or is plugged up. You need to invest in a coolant filter if you plan to keep the stock oil cooler setup. This will filter out fine silicates that will clog cooler. Clogged oil cooler leads to flash boiling coolant in the EGR cooler which blows it out and can lead to blown head gaskets even without tuning.
FICM voltage is important as well, Ideally should be 47-48v
Has the trucks EGR cooler been deleted? You can delete the EGR cooler and leave the EGR valve in and hooked up, no need to install a block off plate. Mine didn't throw codes going this route (2004 model).
Your truck (if it hasn't been addressed already) will more than likely need stand pipes and dummy plugs replaced along with the STC fitting on the HPOP. Not hard but something to be mindful of the symptoms.
Get your maintenance down, check over your engine vitals with a fine tooth comb, see what you have before you go hot rodding and let something loose that could have been prevented.
Delete it, throw a good tow tune on it, maybe replace the turbo with an 03 model if you want it to sound like a F16 and don't mess with it any more.
I've always been fond of Truck Source Diesel's tunes. I run a tow tune from them now, but also have their Super Panty Dropper on deck if I feel like playing. They are great folks to deal with. A custom dyno tune would get the most our of your truck performance wise but if your after a reliable family rig just keep it dialed down with a tow tune.
Now, if your not scared to spend your kids college savings account and take out a second mortgage for repairs, we can talk about upgrading turbos, upgrading fuel delivery, and throwing a set of 190/100 sticks in there.
Feel free to drop me a PM if you want to pick my brain or have questions, I've spent my fair share of time under the hood of mine.
Powerstroke. org used to be a HUGE wealth of knowledge but I haven't been on that site in a while to see whats going on there now.