The FASS....I would personally go with the system with the filters. This enables you to do away with the stock element filter that is rather small. The spin on filters are really nice. One thing I don't like about the FASS is the noise level. I have only heard one truck with the FASS running, but it was a noisy sucker, too loud for my taste.
The stock lift pump actually works fairly well, up until 375HP or so. Most people get 50-100K out of a pump, on average. I have no plans of changing out mine.
Injectors.
There are basically two types of injectors.
1. extrude honed. This is basically taking a stock injector, pushing an abrasive fluid through the injector at a high speed, and it basically wallows out the stock nozzle holes. These are usually the cheaper injectors, and may or may not cause some smoking at idle depending on the stage. They usually come in 3 stages or so.
2. EDM's. Do you know what an EDM machine is? It cuts metals with a lazer. A virgin nozzle with no holes is taken and holes are then placed where ever the performance manufacturer wants them, and as many as they want, at any spray pattern. Meaning, instead of making 5 holes just bigger like an extruded nozzle, they can just add one extra hole, or two. Usually they are larger holes though. Anothe rbig thing with the EDM style is the spray angle. They say they can gain power without extra fuel and smoke just by changing the angle of the spray! Usually you see a better mileage increase out of EDM injectors, since the spray pattern is different.
Formula 1 are big into the EDM injectors and their Mach line sells well. My dad has a set of Mach 1's in his H.O. (65HP). Think the biggest injector is a Mach 7, which is 210HP ?.?
MBRP is a fairly loud system. I'll let you in on a secret, most of the mufflers out there are the same thing from multiple companies. MBRP, Banks, BullyDog, Diamond Eye...they use very similar parts. MBRP an Diamond Eye offer better value over some other brands IMHO.
As far as the intake, There are a lot of options here, just like the exhaust. AFE and Scotty are the most popular aftermarket units. The scotty sucks from the cowl, but you have to cut a hole in your firewall for the inlet and I hear the whistle is stupid loud inside the cab.
The home made BHAF (big honkin' air filter) is a very popular choice that is a cheap alternative. It consists of a huge Donoldson universal cylinder filter that as a 4" inlet with a lip on it. You slide a piece of 2" long 4" exhaust pipe into the filter and onto your intake tube. This gives a flange for both pieces to grip. You then can purchase a heatshield from a guy on a few different diesel forums, but I wanted something better like the AFE style and made my own. For I have a whole $65 in my intake setup, along with a dew hours labor. If I really wanted to flow lots of air I would have just ordered an Amsoil washable guaze filter like the AFE/K&N/Volant instead of the BHAF and had the same thing.
Although I like my dad's H.O/6spd like yours, I prefer the modified autos myself. 
Dang, I spent like 1/2hour writing that. It was seriously LONG...
The media is a thin nanofiber material designed by Donoldson and is reusable by just blowing it out with air. I kind of wish I would have went with one, but they had just come out with the line when I was doing my BHAF. Plus, they only come in blue, I want red....
