As long as the basics are there (from what you mentioned was still on the motor yesterday, it is there) then you can get a brand new full stand-alone harness from howell. If the computer is there with the motor, at least grab that too. When I bought my 8.1 off craigslist...it didn't even come with a harness. I called Howell up and had them make me a brand new one to my specs of what I needed and that's it. I think that harness is worth it's weight in gold right now. The only issues I'm dealing with getting my 8.1 to start are not related to the harness, but other crap I'm dealing with. If you can get the motor that cheap, spend another ~$1500, maybe a little more (harness, tune, conversion motor mounts, fuel system, and exhaust) and you are around $2000 for a significant upgrade in power plants in your crew cab while keeping pretty much the same mpg's if not increasing a little bit....
In reference to the 6.5 diesel pedal...it's an option unless you want to keep your 700r4 behind the 6.0. In that case, I say either keep it a throttle cable (if the motor is right now) or convert it to a cable driven that way you keep the TV cable operation for your tranny. When doing these types of swaps, factor in another at least $1000 in misc crap you will need to get it up and running as the nickel and dime crap come up when you swap. So if you are ready to spend around $3000 to get everything done (could be less...just depends on how good of condition everything is), I say go for it. These swaps are a dime a dozen now a days and there is so much tech out there its not even funny