Yeah I can tell by your sig that you like to do things right. The 6.4 is pretty stout but like any engine it may have some problems (but nothing like the 6.0) The only truck I would stay away from is a Job 1 which are the early built 08s. They are still good trucks but it seems like you hear of more problems from them. Now that i've said that, there are also guys on here with Job 1s that have had them tuned for many thousands of miles with no problems. If you find a 6.4 that you like, get the VIN number and have someone run an OASIS report for you. That will tell you what work has been done on it by the dealership.
Now back to the performance side of things. The tuner is pretty much up to you. I have heard good things about H&S and the Livewire with custom tunes. I can personally say that i'm happy with Spartan. For exhaust I would recommend a 4in downpipe into a 5in down pipe back straight pipe(or you can run a muffler on it, its purely a sound thing). Now for intake, I like my S&B but AFE makes a great product. There are vendors on here that will make you a good deal on a package. I have heard good things about rudy's diesel performance but I personally deal with Trey at cowboydiesel.com. He is getting his business up and running but he has great communication, fast shipping, and good prices.
2015 CCLB F350 Dually King Ranch - SCT, Flo-Pro, No Limit Fabrication, Recon, Atomic LED, Weathertech, Fuel Offroad, Toyo, Magnum Manufacturing, SouthernLite LED
2008 CCSB F250 FX4 6 Speed - Spartan, KEM, S&B, Diamond Eye, Southbend, Javelina, Ranch Hand, Bilstein, Toyo, XD, N-Fab, Southernlite LED, Recon, Kenwood, JL Audio - SOLD
2005 ECSB F250 - SCT, MBRP, ARP, FCDP, S&B, Autometer, Swamp's, Recon, JL Audio, MTX, Bushwacker, Westin, XD, Toyo - SOLD