Thanks for the update.
I'm guessing you didn't see +5v on 1, 51, or 53? I'm measuring +5.5V on those during active use......
I'm also seeing +3.6-3.8v on 5, 44, 47, 94, and 97. Many of your missing pins is this lower voltage (rail?)
Perhaps it's the closet romantic in me coming out in old age, but isn't the layout of this FX2 pinning absolutely beautiful? So perfectly ordered? Especially the section of pins between 11 and 89 on both sides of the connector?
You get groups of 6
+5v, data, data, gnd, data, data.
+5v, data, data, gnd, data, data.
..... and so on....like 10 or 12 groups like that
and the data/address bus going in order from AD31 down to AD0, alternating sides. 30,29, other side 28,27, other side 26,25, other side 24,23. So cool!@!@#
The layout almost is in itself built in documentation, like XML almost, that the form of it ensures the correctness. I know there are rules about evenly laying out grounds to prevent "charge dumping" (just heard this term) and similar ideas for the power rails.
It only gets messy at the ends of the connector, where there's more variability and less grouping/structure.