I wonder if not everything is explained or published in that document.

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The stuff on bitsavers has massive holes in it. (A particularly irksome thing that comes from comparing the March and May-dated versions of the protocol documentation is the earlier one specifically suggests that the protocol contains "acks" transmitted through the IWM from the drive to the computer, while a conservative reading of the May document suggests that handshaking is limited to that business of "toggling /HSHK", which is semi-infuriating because it's not entirely clear how /HSHK works.) There may be no way to definitively fill in some of the grey areas without constructing a probe and doing signal capture and analysis on a live and working HD-20. Unfortunately.