Lord knows I have been there too. There is a lot that could be going on there. Try to isolate what's changing in each iteration. First I would run the test with no adjustment 2 or 3 times. Do you get the same reading each time? If not then stop and figure out why because your chasing your tail already.
If you have the tramming aids installed and tightened down then it's unlikely that the head is actually rotating on the boss on you, even less if you keep the head bolts snug while doing this. My guess, and it's just that, is possibly a lose gib that is allowing the Z saddle to rock a bit as it moves up and down, maybe even a little misalignment in the Z nut mount and screw. I cleaned up the movement in mine early on by running the head all the way up the column and rotating it over to access the bolts that connect it to the Z nut. Loosen those up so the nut mount can slide into alignment and then re-tighten them down. That should put the screw and nut into line if they are off.
After that I tightened up the Z gib by running the head down to a wood block and letting it come to rest against it without forcing it into it. Then proceed to tighten in the gib maybe even a bit too tight. Then I ran it up and backed it out until I could move the head 0.001" on the big hand-wheel and have the head move that much, no stick-slip. That was the best I could do.
I always had a similar issue. The head would rock slightly when the locks were set so I had to develop a feel to how I set it. I set the top lock which seemed to effect little. Then I set the bottom to a consistent position because it would change the tram results depending on how it was set. Definitely don't crank the hell out of the locks. You shouldn't need to do that at all to get it to hold when the gib is adjusted right.
I've been in this hell before too. Took mine apart to get it into the basement and boy-oh-boy did I have a heck of a time getting it back into tram again. You can really get lost in the weeds quickly.