The way we did it the shop I worked at is to pull the timing advance off and make sure it isnt slipping. Then pull the injectors and have them tested, but dont change them unless there is a problem other wise it will take about 60000 miles for them to open up and start to run right. Test the afc and make sure the diaghram is good, we would just put a kit in it. Get the valves set and make sure they have no drag on the feller guage when its done, but you dont want they to click. Get the fuel settings set to high side stock. Now have the timing set to the top quarter of the timing graph and set the afc. Have the aftercooler tested for leaks, We would see alot of them broken and leaking. Test the fuel pressure with a manual guage should not drop below 20psi in a hard run, also make sure the aircleaners are good. Last you might think about putting a pr4 valve on butween the air compressor and the airdrier, We found that boost would go out the bottom of the airdrier when it was open. The pr4 has a spring in it set at 40psi so that it takes 40psi to open, the boost wont do it but the compressor can with no problem. This would make most of the drivers very happy, If you want alittle more you can try to get them to go 10% over but usually it wasnt needed. This should give you good power and economy. On the injectors if 2 or more are bad put in a set so the engine stays balanced, And like I said new injectors are not a bad thing it will just take a while for them to break in. Good luck and let us now.
Mike