Sounds like you have a good plan already, but due to the high pressures in common rail engines, it is recommended to replace the injection lines when they are broken loose. I would flush and bleed the system like you talked about, but disconnect the return line to the tank, then start it and let it run for a minute or 2, or until nothing but diesel comes out of the return line.
The specific gravity of gasoline is lighter than diesel, so if the truck sits, you could bleed the system and it would run fine, until you "shook" the tank and mixed the gas and diesel, then it would start running like there was an issue. I've run into this a few times on equipment. I'm guessing that's why your brother's truck has run, then didn't.
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'05 GMC 2500HD, CCSB, LBZ mouthpiece, A.R.E. cap, N-FAB nerf bars, 265/75/16 General Grabber AT2s, B&W Turnoverball, leveled tow mirrors.
2012 Silverado 1500 ECSB