Re: Wait!  The ripple is there for a purpose.  The glass was installed to
protect the stained glass from the ravages of weather.  and...
I would leave the ripple glass and concentrate on making it more airtight.
and...
There has been deterioration between the layers because of condensation,
and it is best eliminated, if it can't be vented.

I agree,  Wait!  The issue and technology of whether and how to vent
protected stained glass windows is hotly debated among stained glass
specialists.  The best study I have seen is by Art Femenella, but theories
and solutions abound here and in Europe.  What I do know is that to trap
air between an outer and an inner plane can be deadly to the art glass
system, without due consideration to temperature build-up, expansion and
movement (expecially the daily and seasonal cyclical movements, most
especially in temperature responsive lead), convection currents,
condensation, weeping, vent-in, vent-out, etc. etc.   Think it through.
Exposing the stained glass can be a mistake, but the worst thing you can
do, in my opinion, is to seal a piece of heat building,
bound-to-fog-eventually sheet plastic on the outside.

The most clever use of glass I've seen on a turn of the century building
was on the roof of the north wing of the Villard houses (Random House wing)
here in NY where there were cast glass tiles identical in profile to the
curved spanish clay tile of the roof set on purlins allowing lignt in like
a seamless skylight.  Something went wrong, because by the time I found it,
it had been slathered over with pitch and broken up by the re-roofers.
--Jim R