Kyle,  My friend Jeff Vincent and I have restored and tuned quite a few
Molinari organs.  As Robbie said, this organ is not chromatic so it's
a bit confusing if you're used to a typical pipe organ.  Not only are
the pipes diatonic, but they are not in the right order.  Well, some of
them are and some of them aren't.

The typical tuning for a small organ like this is all naturals and one
sharp.  There is a typical tuning scale in "Treasures of Mechanical
Music".  If nobody has messed with the pipes, you can make a tuning
chart to verify that your organ is the same.  Mark off about 3 octaves
on each scale -- all the notes, evenly spaced.  Chart the supposed
notes (x-axis) against the actual pitch (y-axis): B, B+30c, etc.
You should get a straight line.  Okay, the line won't be very straight,
but the process will tend to show where the straight line should be.
Plot the open pipes on a separate line.

Pay special attention to the open pipes as they tend to be mostly in
tune.  And you'd have to physically alter them to tune them, so the
less you cut back the open end, the better.

Also, forget the standard A=440 Hz or A=435 Hz tuning.  On a late
model organ, it might be pretty close, but an earlier instrument could
be anything.  Just look at the open pipes and chose a 'standard' pitch
that requires the least cutting into the sides of the pipes.  You'll
have to close up the ends of a pipe to lower the pitch but you'll have
to cut the end back to make the pitch higher.  Set your tuner to offset
the amount you determined above and adjust the open pipes to the
straight line.  Then adjust the closed pipes to match.

In reality, it isn't usually this simple so if you have any questions,
feel free to give me a ring.

Regards,

Craig Smith - from western New York [at the edge of Hurricane Irene],
where we're getting a little wind this Sunday morning!