I think you may have two problems, but first let me say that I think that your "improved" reading was also relatived to the fact the the engine was "warmer" but not at full operating temperature.
One problem is a dirty injector or injectors, and in all likely hood a problem with your linkage/throttle cable.could be inj plunger height too...o
To properly tune a Detroit it's gotta be HOT,to properly check it's rpm...it's gotta be HOT.to run the rack...valves...HOT.
I think you need to chk your RPM at the crank too.
Chking a rack adj is alot easier than adjusting same....start here.
turn pages at the top....http://miscpartsmanuals3.tpub.com/TM-9-2815-224-34-P/TM-9-2815-224-34-P0486.htm