Looks like a nice starting point, that truck looks pretty solid and straight, so that shouldn't be a real problem.
The core support thing, heck, if you had decent metal fab skills, and a tubing bender( a small one, capable of square tube can be had from Harbor Freight, Northern Tool, Eastwood, TP Tools, etc. for less than $200) could make easy work of making the lower loop under the radiator, and could be used for MANY things on that rig( trans cross~members, brackets, frme reinforcement, etc).
The axle plan sounds good, though if you wanted, a D70 or D80 might suit your desires as well, or even a Ford/Sterling 10.25 or 10.5 rearmight do it( they were in one tons and duallies, so....).
The power thing, well, those numbers should be reasonably easy to accomplish with the parts you've listed, or pretty close.
The reliability thing, it sounds overly-simplistic, and like a 'duh thing to say', but go through and remove the weaknesses, one by one, the more weakness is removed, the stronger the truck will be. Everything that might be a problem or is a known problem, like you said about the wiring/electrical stuff. Not that this bit helps much, as it doesn't.
About the costs, that is a pretty good budget I'd think, though watch out for the 'nickel and dime' stuff, the nuts and blts, and belts and hoses and all that can and WILL add up quick. Though since if you're gonna go through and rebuild this rig, you'd probably be better off by not painting the frame, but rather using a product like Eastwood's 'Extreme Chassis Black' or Bill Hirsch's Miracle paint, or even POR 15 to really protect the frame. Not to sound too overly simplistic and stupid here again, everything you wanna do to this truck, it's gonna be built on that frame. I mean with auto paint costing easily $20 a gallon, the extra cost of say $45 a gallon, you might be better off doing it, as you'd only need like maybe 1-2 gallons, I'm not sure about the coverage rates and such. Or maybe even use something like that 'spray-on' -type bed~liner product, because you'd do well not under-estimating the value of the coating on the frame.
The time-line thing, as long as you keep that pace, you might make all your goals.
The comforts thing, it looks like a good place to start, so that might not be too hard, though I don't have a good idea on how appointed your 2001 truck is, so....
If you have decent metal-fab skills, and you didn't like the looks of that year group, you could fill -in the headlight bucket areas, then blend out all the bodywork there, then incorporate something like the poster above said with Jeep-syle round lights, or even put something like a 'Dodge Challenger-style' of recessed headlight/grill area. Or you could also ut the front from an older 'slant-nose' style on there, though I'm not 100% on all of what would be needed for that one.