OK, I've fooled with this off and on for the last month.
Voltage coming from the p/s molex is really constant over about 6-7 readings, always around 5.18. No problems with the p/s obviously, especially since it's already been replaced (for no reason, I guess).
Readings looked like this for 6 measurements:
5.18 5.19 5.18 5.18 5.18 5.18 (voltage from p/s molex across all readings)
5.09 5.10 5.06 5.10 5.10 5.07 (measured at jamma connector across all readings)
5.09 5.07 5.01 x.xx 5.04 5.02 (far end of jam extens harness; x.xx = i didn't measure result)
4.97 4.96 4.92 4.96 4.94 4.91 (reading from rom chip on pcb)
Most of the time the voltage at the rom was quite steady around 4.97; I only measured the other voltages when the rom voltage moved around which wasn't very often.
Now the interesting thing is that the voltages would jump all over when i squeezed the jamma extension harness into the jamma connector. And they'd jump around when I'd probe the jamma pins with my DMM leads or move the jamma extension cable around a bit. And the values will jump around when I hold the harness and wires down so it won't move but push on the power wires with my finger.
Some of the jumps were kind of disturbing; when I probed the wires and move them around slightly I saw variations at the rom from around 5v down to about 4.8 (it moved as I pushed on it).
I just pulled the jamma extension harness off and hit the male end (plugs into the jamma cab connector) with Deoxit and Deoxit gold. I got some grime off the cable when I cleaned it and it seemed to perhaps help a bit with the numbers jumping.
After cleaning and trying to isolate things so I was only pushing on one thing at a time I was getting jumps of around .08 when I pushed on wires.
I'm pretty sure this is the source of my jumpy voltages even though the numbers would also move around a bit by themselves even when not pushed (see the table above). Not sure what more I can do on the Jamma extension harness side so this weekend I'll re-do the +5 and ground wires from the connector from the p/s into the jamma plug with new 18ga wires and .084 and jamma split pins.
The numbers clearly move when I push on the wires/harness connector and that's likely what was behind the voltage changes when I switched games as it surely changed the tension on the wires a little. But the voltage would move around by itself even when I hadn't switched anything. The $1,000,000 question is if the jumpy voltages when not changing cables is from the same thing as when I press on the wires?