I am not sure whether you have 1, 2, or 3 distinct problems. (Your explanation is clear, I just don't know whether they are, at their root, the same problem or not.) I suggest you use a packet sniffer like tcpdump or wireshark to see what is going with the long delays. If using it at one end doesn't provide sufficient information, try it at the other end as well.
You might also get useful information using the -v option with ssh. Use it up to three times for increasing verbosity.
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