I'm a little late to the party with my 2 cents, but I'm "bulletproofing" my 6.0L now. At 122K miles I blew my EGR cooler, which was evident by the white billowing smoke from my exhaust and confirmed by the coolant in my Y pipe and intake manifold. These are the repairs I have done and those I am in the middle of doing in chronological order. (It may not be the best order, but it worked for me):
Superchips Flashpaq, used and unlocked for $200 (but I'll be upgrading to a SCT X3)
4" Dynamax exhaust, about $550-600 from NAPA
Blue Spring upgrade, $60 from Tousley Ford (easy 45m upgrade)
EGR Cooler and Oil Cooler Kit, $2200 from Bulletproof Diesel
ARP Stud Kit with all the injector ORings, $1089 from Bulletproof Diesel
Professional Kit (HPOP upgrade, turbo drain upgrade, oil pump switch, misc orings, gaskets, filters, etc) $220, from Bulletproof Diesel - spent so much at BPD they gave me a free jacket.
Waterpump with CNC aluminum impeller, $250 from Bulletproof Diesel (this one you don't have to do, I just didn't want it going out after a coolant flush and end up wasting all the money on new coolant)
Once its back together I'll do a coolant flush for about $100 (water, Restore, coolant, Fumoto valves, etc) and install a coolant filter for about $170. I have the typical rough start in cold weather, but I think a FICM reflash will take care of this.
I am fortunate enough to have a place to work on my truck with a lift, so I pulled the cab to do it all and did the labor myself. I will have about $5000 into "bulletproofing" my truck when I'm done...until I blow something else up on it.
Bare in mind, I'm pretty new at this and am, by no means, a mechanic. There are certain to be some differing opinions on this forum, but if you budget for about $5000 in parts and a few more $$ in labor you will have a pretty nice truck.
Keep reading this forum. There is a lot of great information on here, but if you're doing the work yourself you may also want to purchase a service manual ($180 on Amazon). You can find most of the manual here and there on this forum, but its convenient to have one on your workbench.
I was told not to buy a 6.0L when I bought mine, but despite the drawbacks its one fine truck. Good luck.
I can tell you what I have done to mine. I have a 2006 F-250 Lariat Fx4. Bought it with 123500. The dealer I purchased it from installed new Bulletproof diesel ear cooler and ford oil cooler. I then installed coolant filter (diesel site) New radiator with Final charge coolant, Installed full gauge set, Auto Meter- Fuel, get, boost trans, got a scan gauge II set for Ficm voltage, Hpop, Oil temp, water temp, I have installed 2 additional trans coolers and bypassed the one in the radiator (can't break 155 degrees to save a life) Harpooned the fuel tank and replaced the fuel pick up, installed the blue spring, ZooDad upgrade, 6.4 banjo bolts, Mobil 1 5/w40 oil exclusively every 5k, installed Amsoil oil bypass with small remote cooler, installed inline trans filter behind grill next to coolers, 1.5" leveling kit up front, 2" in rear, Leer Xr100 top, LED headlights and Fogs, Flush mount LED reverse lights, American racing Wolverine 20x10 wheels stock size tires, stock exhaust, Cat delete kit, Factory shocks, skyjacker dual stabilizers, factory single still installed, Cold air intake, Built a power flush gun and revers flush the oil cooler every 6 months or as needed. Temps are 3-5 degrees delta at 70 MPH. Houston performance diesel did the dummy plugs and risers in 2014. truck runs better than ever. I will say that one thing that keep this think happy is regular oil changes, Motorcraft filters exclusively (No Exceptions) and a regular 12 ounces of a reputable fuel injector cleaner/additive. Also hot shots secret stiction eliminator and (fuel treatment twice yearly). Keep the injectors/fuel/coolant/oil clean and fresh and the truck will take good care of you) I love mine!