I'd do every rubber line under the hood (coolant, fuel, and hydraulic) and use spring clamps (like the factory did) except the few places where a worm clamp is appropriate. Even if you don't want to go that far, please do that 3" long coolant hose that runs over/behind the fan pully bracket. The one that returns the turbo coolant back to the bypass tube. The ones in the valley can be tackled later but that one is a tough cookie on its own.
I guarantee the turbo thermostat has enough crud in it that it's stuck open.
Your water pump looks like it might be newer than the truck. Your harnesses also look like they aren't shedding brittle loom like mine were, before I redid everything I could touch.
An updated oil cooler if you have heavy towing aspirations?
Not the OP, but currently in a similar situation, and I agree 100% (especially the bolded).
As I mentioned earlier, I'd already decided to do the soft fuel lines, as they looked pretty bad. Finally swapped them out last night, and WOW, they were awful. I swear I could almost see through the small 5/16" ones on the CP3. I think the inner liner was the only thing still intact. I was going to use the spring clamps, but the replacement hose I got (Shields Rubber 368, USCG approved stuff) was quite a bit stiffer and the spring clamps didn't seem to compress them much, so went with some good quality Ideal worm clamps.
Went ahead and did the coolant lines on the upper half of the motor as well. They didn't look terrible, but again, were quite soft and flexible compared to the new stuff I got. What's $40 more when I'm already $4k+ and 30 hours into it?
Didn't mention it in my post earlier, but I also rebuild the filter head. Again, what's another $20 while it's already off the truck? And based on how square-shaped all the round o-rings were, I couldn't believe it wasn't hemorrhaging fuel everywhere, especially under 7-8 psi from the lift pump.
Funny you mention the harness. Mine was in shambles, and getting worse every time I only looked at it. Almost just said 'eff it', but my OCD got the best of me. Pulled the engine harness off and completely reloomed it. Did the bundle coming out of the fuse box as well. Used the TechFlex F6 split braided. Quite a bit of work (tedious, too), but OMG, may be one of the most satisfying things I've ever done on a truck / car. It looks amazing.
Considered doing the water pump, too, as I know mine is original (260k miles). But it looks like draining the coolant is about the only common step with changing the injectors. Kinda like the OP, I've been piecemealing this project for a couple hours at a time for the last several weeks, and I'm ready to get it finished. So that'll be a job for another day.
Thanks for the advice, and a bit of reassurance that I'm not crazy for adding on all this extra time / money / work to this already big job. Hope the OP feels the same way.