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Hi Ian,
The Dome equator being 100mm above the bottom edge makes sense to me if they are referring to the mounting ring I use. To me Dome equator would be were the dome wheels touch a surface to roll on - this is what I used, then entered a negative number because my my mount sits well below the wheels rotating the dome.
I have tried (just last night again to) use the exact mid point between the RA and DEC axes (which as you say is inside the mount), and checked when I measure from the dome centre I used only the North / South and East / West components of the mis-centring. My lab is square and faces North East, so when you are inside it its easy to think the house is East of me instead if South East! I fixed this up on the second set of measurements. Last night was my third set - this time I used string and levels to mark the exact dome centre at the height of the mount axes centre point. Turns out I was 4" not 2" East of the Dome centre and my South measurement was off by an inch too. So hopefully this time I have nailed it better.
Homing in a set direction sounds like a good work around to me. If the motor turns thru another change in reflectivity mark that should only be the maximum of half a revolution - which to me would be say 10 - 12 mm.
With only one imaging session (NGC 2070 for two hours) managed successfully (using the old geometry parameters). My approach was to slew the dome, check for dome / scope mis-alignment, then alter the dome home position Az reading in software by a few degrees - and let the dome re-position itself to the scopes. After two goes this had the dome perfectly orientated to the scopes, and after two hours they were still well aligned. Is that the approach you and others use for imaging to centre the dome if your geometry is a bit off?
Another mistake I had made was trying to use the scopes Az when pointing to the middle of the dome slit in its home position to determine the home Az; but as the dome and Mount rotations points are mis-aligned I presume the domes position for say East with be a degree or two further left than the scopes bearing for East!.
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