Attached is a section from the nearly identical HM2000 manual. I don't know if you can read it but the first section says
Quote:
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The 23VA transformer has three independent secondary windings, two of which provide the two isolated, pulsed DC, controlled outputs for train operation
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That means the block diagram in post #2 is essentially correct. It also sounds like the speed control method is via an electronic PWM controller rather than an old school analogue rheostat.
The 'D' connector on the left hand side is meant to supply 16VAC to any extra controller you might plug in there but it is also a handy place to check that the 16VAC which should be going to the internal left hand speed controller is actually there, since the 16VAC for the internal controller on that side comes from the same transformer secondary winding.
I doubt whether the D connector carries anything more than one side of the 16VAC and the other side of the 16VAC. If I'd chosen the wiring scheme I would have made all the pins on one row of the connector AC(1) and all the pins in the other row AC(2). Power it up and look for 16VAC first on the RIGHT hand 'D' connector since you know that channel works. Once you know which pins should have 16VAC on them, look for 16VAC on the same pins on the left hand 'D' connector.