I think you already know the answer...time to move on...
My Buddy has the same vintage 6.0l and has been through the same thing. I'll bet there are a lot of low mileage 6.0's around for that reason. His has been sitting in his yard more than he drives it...he picked up an old beater S-10 as a daily driver...he is a union carpenter and needs a truck...but he cannot trust that Ford. He has ~ $13k in repairs into it. He can't afford to sell it(too great a loss) and is afraid to drive it...he doesn't know what to do...so it sits there.
I think you'll find all the new trucks are awesome. If you don't want to deal with emmsision you are limited to pre 2007.
If you want new and a stick, I believe Dodge is your only option.
But that begs another question; why on earth would you want a manual tranny when there are autos like Allison, ect available now?
These new autos are incredible.
Any way, good luck. I know what I would do...
B