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Ulf,
You need to implement just NTP. You should implement the protocolId() method to return the NTP port number (123) when the input param type is ProtocolIdTcpUdp (see textproto.cpp for an example). While building the packet, stack NTP on top of UDP and everything should work fine.
You can implement it in C++ (see http://ostinato.org/wiki/ProtocolBuilderHOWTO for reference) or as a UserScript (see http://ostinato.org/wiki/UserScriptHOWTO for reference)
None of the existing protocols have a 64bit entity and hence haven't used uint64, but it is possible to use it. You can also use it as two 32-bit entries as you mentioned.
Let me know if you have any further questions.
Its the other way round.
Since Ostinato is a traffic generator, the NTP protocol itself needs to specify (user selecting via the UI) whether the packet will contain the optional authentication. If the optional fields are not to be included in the packet, fieldData() for those fields will return a zero sized QByteArray as FieldFrameValue. UDP can then correctly calculate and put the length value in its header.