Not the guys you are looking for but here goes anyway. It is only a subpanel if it feeds from an overcurrent device. In the State of Nebraska they say that the farm loop with a generator transfer switch or just plain disconnect on the meter pole is not the first disconnecting means, just a convenience disconnect. This means that any shed or house that feeds from the meter pole is a separate service, not a sub panel, unless there are 2 panels in that building. Therefore you do not have to worry about separating the grounds and neutrals in the panels.
In regards to your grounding issue at the one shed on rock, by code you are allowed to use a grounding plate. This is just as it sounds, a metal plate of the right size(someone else chime in here with the size) and has to be completely buried. I am not too familiar with this type of grounding since rocks here are awfully scarce. If you grounded the reinforcing wire/rebar in the concrete it would help also. I would guess with all the ground rods that you have driven by the waters' it is grounded plenty good. Just FYI, the code book says to have any concrete and metal parts(gates/fences/etc) all bonded together so that if one is electrically charged there is not a really good ground by touching the other, the technical name is equipotential plane. Kinda like getting shocked every time you touch the range and the sink, the range has a little short to the ungrounded frame and when you touch the metal grounded sink you make the path.
Hope this helps a little. Glad you are trying to do it safe.