Physically fitting the engine into the engine compartment should not be too bad since you will have the ORU straight axle conversion.
???I have put 5. 9's into both IFS 4wd and 2wd trucks with no bodylifts or axle conversions. The most I ever had to do to the IFS diffs was slightly shorten the cooling fins on them to allow oil pan clearance. They will fit fine without issue. With the IFS gone, you should be able to drop the engine low enough to clear the hood without the need for a body lift, and you should be able to set it far enough back to run a mechanical fan.
I have installed factory Dodge Cummins clutch fans, using a dodge radiator and innercooler. There was some modification to the core support needed, but nothing major. If I remember right, I installer the innercooler on the front side of the core support along with the A/C condensor. The hoods always closed up, with IFS suspension, and no body lifts
Since your brother is a diesel tech, getting the engine hooked up and running should be a piece of cake.
It's the details that you will find will occupy your time. Getting all the gauges to work, cruise control, tach, etc. will be where you will spend a lot of time. For me, the time required to figure out the details just was not worth it, and that is why I brought my truck to Autoworld.
Before I got sick, I used to work with Kenny, you made a wise decision to hire him to do it. He makes sure it will last beyond the engines life, not the typical GM trucks short expectation. The newer GM alternators are also the pickup for the Tach's, which makes it easy on the newer trucks to convert, The harness doesn't need much modification other than lengthening the wires. You just need to install a wider serpentine pulley on the alternator and fabricate the accessory mounts to get it onto the
If you have any specific questions, I'll be glad to help. I may not be able to immediately answer them because I'm not going to see the finished product until mid to late December when I get back in the country.