Hi, Here the answers to your observations.

1)  The 2-tier stack is the later version.  It should have round valve
seats, and also the pneumatics are usually all the same size and not
graded.

2)  Pneumatics were always glued onto pouch leather by Aeolian, and this
is original.

3)  When completely rebuilding, it is easier to remove the tubing from
the holes, but then again, if you want to do that some other time, you
will need some patience if the tubing is stubborn.  Sometimes a
soldering iron helps.  I would not suggest sanding the nipples as they
are nickel plated.

If it is really bad, you can heat them with a soldering iron till very
hot and then pull them out completely once the shellac melts.  You can
them clean them by using a heat gun or some chemical like paint
stripper.  Thereafter you can re-install them with new shellac.

Do you have the metal Duo-Art/pedal switch, or the wooden blocks like
in the American pianos?

Regards

Bernt Damm
Cape Town