Hmmm...I don't have a 10 series repair manual in front of me, however you may have mis-read something.
First, you don't check the output shaft (the 540 or 1000 RPM shaft) end play. Even if you did, you can't change it. I suspect that the .003-.005" end play spec is for tractors with single speed PTO, which you do not have.
Next, the .001-.029" end play spec is for the upper long PTO shaft that splines into the PTO clutch. This can only be checked with the top 3-point cover removed, or through the LH side cover.
Finally, the upper PTO cluster gear end play is going to be around .005", and not much more than that. If you have upwards of .030" end-play in that thing, that could well be the reason for your rattle.
I would STRONGLY suggest that you take another look at the manual to make sure you didn't make a big mistake. If everything is setup properly, there should be NO rolling torque of the final PTO assy (other than seal drag), assuming the upper drive shaft is not installed. If the upper shaft is installed, you'll be reading PTO brake band drag, which is going to differ depending on which output shaft you have installed.