setting it to what it actually reads (if it has 36.5 vdc after 15 minuites operation, set it to 36) will help a lot with getting the right voltage readings even if you don't set the internal resistance compensation (function 14).
95% charged to 60% (after 3 hours operation) charged sounds "close enough" to me, especially if the battery is not new.
Remember those numbers you asked about near "the main plug side "what does the o2-1b-vg on the main plug side"?
those are numbering that is particular to the type and make of truck, so that is the one set of numbers that should be the same between the different EV100 cards that will work in the truck.