Here's the list for a "tuneup"...
1. Check cold exhaust valve clearances.
2. Warm up engines.
3. Recheck hot clearances. Make sure engines stay hot during this test (not always easy)
4. Check governor gap and adjust
5. Check injector racks, adjust.
6. Set throttle delay.
7. Check high idle, adjust. If off more than 50rpm, go back to (4) and start over!
8. Check and set idle and buffer screw.
If you haven't already, I'd also pull and clean ALL the coolers, with the possible exception of the oil cooler.
I would check the clearances and injector height/rack....
... even if all appears ok.
None of those checks are invasive or require CHANGING anything. Exhaust valves in particular are critical; if they're too loose you can have a keeper come apart under load, and if too tight you can burn one. Either is a very expensive problem.
Pulling all the injectors is not something to do unless you have a reason to do so. Contrary to popular belief unless you get crap in them (due to bad filtration, water in the fuel, etc) injectors do not go bad for a very, very long time. Its fairly easy to damage the tips during removal and its even easier to get crud down the open holes or screw something up taking them out and replacing them, not to mention that if you yank 'em you now have to do a complete turn-up by the numbers.
Agree you need a shop manual, and a couple of special tools (injector pin-timing gauge, etc) None of this is expensive.
I go through the tune on my engines every year. I've yet to find things EXACTLY where I left them.