Lots of folks have asked about ribbon connectors of various types in the forum, but I have some significant moisture and vibration issues to deal with so I suspect I will be forced to make them by hand before they become available. I would like to pot the entire stack in resin, and jumper across to another protoboard, to allow the FTDI communications after the main stack is turned into a solid lump.

Has anyone else done this yet? 

Do I have access to enough lines for the FTDI communication on those protoboards, or are there "hidden" connection lines in the stack connectors that I cant replicate that way? 

and finally:
Any other things I have not thought of yet, like "How long can those wires be before I induce other problems from things like line capacitance."

1> if you want FTDI communication, then you would have to get that from the USB shield, I don't think that FTDI info is being routed through the header connector.

2> If you use ProtoShield 1 then you should have access to all 40 pins that are in the header connector.

3> If you find that you have to much line capacitance when using a ribbon cable then you could look into using some other type of long rang communication, for instance I2C, that should be good for 6m. Also check out this thread: http://forum.arduino.cc/index.php?topic=57604.0

Right , so if I jumper every wire on protoboard1 directly to its equivalent on another protoboard 1:

I can hook this to the main stack, and then pot my main stack in epoxy leaving one end of the two connected protoboards exposed, and then hook the ftdi board to the exposed end and have communications to the cpu, even though it is now encased in resin.

Of course, even the thought of soldering 40 individual wires beside each other at that scale is painful.

Right , so if I jumper every wire on protoboard1 directly to its equivalent on another protoboard 1:

I can hook this to the main stack, and then pot my main stack in epoxy leaving one end of the two connected protoboards exposed, and then hook the ftdi board to the exposed end and have communications to the cpu, even though it is now encased in resin.

Of course, even the thought of soldering 40 individual wires beside each other at that scale is painful.

We do have these: https://tiny-circuits.com/shop/tinyshield-proto-terminal-blocks/
They have 30 of the 40 pins.

Oh and those tiny white 40 pin connectors, I can solder those by hand Well, I have to when the pic & place machine missing them.