OK, alright, for anyone who finds this, and has the same cognitive block I did, here's my answer and hopefully it helps you.
Right hand rule: (as Rob has pointed out many times), um rules: so...
Top of Machine is low negative, and gets more negative as you go down.
Left of machine is zero, and gets more positive as you go right
Back of machine is High Positive, and gets more negative as you come forward (this was my Y axis and my first sticking point)
Depending on wiring and screw shafts and belts and whatever, you have to determine which way to move your axis so that it obeys that convention.
A test with writing will help, since it will be mirrored in some direction if you have your motors going the wrong way.
See: ~/linuxcnc/nc_files/examples/3dtest.ngc and /usr/share/axis/images/axis.ngc
To reverse a motor/axis (I needed to do this to get myself right: I was 'writing' the logo mirror-backwards in Y) the easiest thing is to go to your .ini file, to the [JOINT_n] for your axis, and reverse the sign on STEP_SCALE. (There are other ways, reversing wiring, etc, but this worked for me and is easy to undo and all my wiring was otherwise identical, so I preferred a software solution.)
Then you need to worry about homing. If you had it working before (as I did) then you'll need to reverse the signs on HOME_SEARCH_VEL and HOME_LATCH_VEL (Mine went from positive to negative).
Finally, and this is the one that bent me a bit. (And I see Aciera has jumped in to help me while I'm writing this, and I thank him very much, but I don't think the answer is quite right for me... I tried that and it wasn't very good.)
You have to make sure you're honoring the right-hand-rule, which means whereever your sensor is that trips to signal your axis has reached it during homeing, should be numbered accordingly.
The part I had to wrap my brain around was that in my case, this means it's:
HOME_OFFSET = 300
HOME = 290
MIN_LIMIT=0
MAX_LIMIT=300
I was trying all kinds of HOME_OFFSET settings waaay too close to zero.
Now my machine red lines are correct, and loaded files show inside the machine, and all the axes move the way they're supposed to.
It even 'air carves' LinuxCNC as pretty as can be.
Thank you thank you Aciera!
Cheers everyone!
