You do not need a computer. you need a mechanical injection pump, a db2. My truck has a transmission control module for the 4l80e (e being electronic) and a tccm (transfer case speed deciphering component) nothing else . Since you have a manual transmission you need anything electronic except a speedometer, unless you put in an old cable driven aftermarket, which is what I would suggest. Eliminate the factory dash and put in mechanical gauges, they are more accurate and reliable anyways.
The only electrical components for you are starter, alternator, electric fuel pump, fuel shut off solenoid, fast /cold idle circuit, glow plug solenoid, lights, horn, radio. (Am I missing anything here folks?)
You might consider buying a wreck if you are not familiar, that way you can see it all during disassembly. You still never mentioned a budget, you might do that before you get in too far. Don't think it's a quick, cheap, 2 weekend project. You will devalue your truck in doing this on resale for most cases. In Nv. all emission testing is done through the aldl connector after 1996 so here and other states like it it would never be allowed on the road without retitleing, and that would make it a $ project.
You know that the smaller 5 speed will not handle the torque of the 6.5 but you want to run it anyways. sounds like a cash flow problem, and unless you are getting a running 6.5 for next to nothing, you might no be able to pay for all the little things this conversion would take. Getting a starter to work with your trans is a custom flywheel set up or cutting off your bellhousing and welding on a donor that can accept the starter.
Once it is together you will have to baby the truck to keep that tranny alive long enough to pay for that extra work. I believe a donor truck for engine and tranny & xfer case would be cheaper in the long run.
The heavier engine will affect braking as well iirc. Any 1/2 ton 6.5 guys could help verify that please?
I don't want to detour you, but make sure before you drop cash into it.
make sure this is the truck you want to have for a long time before going into it. Good luck.