The piece of wood won't prevent a person from pushing so
much brake fluid out of the system that air is introduced
via the master cylinder reservoir becoming too low.

ISTM that's what happened, and the air entering via the
reservoir enters both "sides" of the brake system. I messed
up a couple of years ago during a routine brake system
drain/fill/bleed and had the same thing happen (pedal went
to the floor while bleeding brakes; but I /know/ I let the
reservoir get too low and introduced air). I re-did the
bleed, and all was well. (There were and are no problems
with my master cylinder.)

I think you fixed two problems: An internal leak in the
master cylinder (fixed by replacing it completely) and air
introduced to the system (fixed by doing a thorough bleed
after replacing the old master cylinder).

I think it meant you introduced air into both systems, in
this instance.

You did add brake fluid at some point during all this,
didn't you?

the seals wear and leak.  fluid passes past the seals - just like a
shock absorber.  it's real simple.  the floating secondary piston
doesn't make any difference to this as all seals usually wear at the
same rate.  the only thing to worry about is replacing and bleeding,
which you have done, and taking the care to flush the system with fresh
brake fluid every year or two, depending on climate.

in the future, if you're bleeding a new master cylinder, don't dick
about with the piece of wood.  the pistons are designed for full travel,
and failure to exercise that on some vehicles means you'll never succeed
in getting all the air out.  the wood theory comes from old wives tales
about "i bled the system and the cylinder failed a couple of weeks
later".  reality is, the seal was shot but swollen due to contaminated
fluid, therefore it kinda-sorta held in there.  clean fluid re-shrank
the seal, which would have happened regardless of bleeding method, and
it started to leak.  not changing the fluid may have allowed it to
survive a little longer, but it was on its way out anyway.  moral of the
story: change the seals/cylinder and bleed properly.  if you expose
additional problems, it's a good thing - this is a critical safety
system after all...

Probably off course on this one, but wanted to make sure... you have been
using Honda brake fluid? Other brands may not be compatible, in which case
you can get that happening. It happened to me when I had a Lotus with the
old Girling brakes and let the parts guy at Western Auto convince me all
brake fluids were the same. The fluid attacked the seals starting with the
secondary seal between the two halves of the cylinder... it had fluid on
both sides. When the primary seal failed the pedal went right to the floor.

Otherwise, I agree replacing the master cylinder was the cure one way or the
other.

Mike

    When I work at the shop where I work part time we have had a
number of master cylinders or slave cylinders fail all of a sudden
while bleeding or changing brake parts and we (me and the boss) think
it is because when you bleed a brake since there is no fluid to stop
piston travel the piston goes further down the bore than it usually
does and dirt and corrosion might have accumulated there to rip up the
seals.  Like 3 months back I changed an old toyota camry rear brakes
and we pressed on brake pedal and started to adjust it.  Then we
noticed it leaked a huge leak from cylinder, had to change cylinder, it
was not leaking at all before.  Only difference was brake unadjusted so
pistons in brake cylinder traveled further in bore to dirty rusty
surface that ripped up seals.  Also I just bled my clutch slave
cylinder, was alone so I had to use clear tube in glass bottle
technique, and I filled clutch master about 7 times and pumped out
fluid.  Boy you should have seen all the black stuff in the bottle.
    Also if you understand how a brake master cylinder works you will
see how if one circuit fails the pedal will go further to floor.  In a
typical master you have 2 pistons one for each circuit.  In normal
operation when you press on pedal it pushes rear piston forward, The
rear seal will push fluid lightly and push front piston forward, then
front piston and rear piston will start to apply brakes.  If front
piston circuit loses pressure then front piston will go into bore till
the metal part of piston hits end of bore and rear piston will also
travel further (remember there is a rear facing seal on front piston. )
Now if rear piston circuit loses pressure then the rear piston will go
forward till the front part of it hits the front piston and pushes it
forward where good forward piston circuit pressure will stop the front
piston and rear piston. If both circuits fail the when you push the
pedal then the rear piston will run into the front piston and the front
piston will run into the end of the bore( in this case the pedal will
travel the furthest toward the floor.