Hi Jim,  I know virtually nothing about the organ Concertola but I do
have a lasting love-hate relationship with the piano version which may
provide some clues.  I expect there are other MMD people who have the
organ version and you may hear from them as well.

There's no point in giving you the tracker port layout since I doubt
very much it would be the same as for the piano considering the vastly
different tracker bars.  Nevertheless, the operation is basically as
follows.

There are five tracker holes involved.  Four of them are used as in the
standard 16-level Duo-Art expression setup and are connected through a
valve block to pneumatics of the usual additive values of 1, 2, 4 and
8.  These are connected by a linkage to the tempo rod in the governor,
just as a manual lever would be.  The "0" tempo is 35, "1" adds a tempo
of 5, "2" adds a tempo of 10, "4" adds 20 and so on up to 110 when all
four pneumatics are closed.  This allows for a full range of tempos
from 35 to 110 in 5 degree increments.

The 5th tracker hole is a cancel which shifts the other four holes, as
well as itself, to the note-playing position.  The transfer valve is a
simple brass sliding arrangement powered by a small pneumatic which
shifts back to the tempo selecting position upon rewind, ready for the
next roll.

The appearance of the tempo holes on the roll is first a horizontal
line of up to four holes in appropriate position for selecting the
tempo, followed a short distance later by the cancel hole.

For the piano a punch was issued (which I wish I had) to make coding
of your rolls easy.  I'm not aware of any "pre-tempoed" piano rolls
although that doesn't mean they weren't made.  It could be that the
tempo holes on your rolls were added later by the owner since they'd
make spurious sounds on a non-Concertola machine as they passed over
the tracker.

Hope this is understandable and gives a little insight into at least
the piano system for you.

Best,

Jim Heyworth,
Sechelt, B.C., Canada