caulking.

Used lots of silicone. Laying on their sides hold water on every pane. Need to find a way to keep the majority of water off the window...

It's a very charming building, but completely impractical. Water will pond in every pane of each window, as well as whatever other depressions or low spot exist in the frame. Then the water will ooze and drip everywhere as it obeys the law of gravity and exhibits capillary action. Caulk alone may delay and lessen the issues but standing water will eventually find a way.

Roofs are designed with straight shot slopes to shed water. You need to create effective drainage for every square inch of your pond system. Keep in mind this is a completely non-approved thing to do. By the time you have adequately mitigated the leakage, you will have wished you did something a little more Home Depot.

Was thinking large panels of plexiglass (expensive), the clear panels mentioned above (inexpensive but not as aesthetic), maybe searching Craigslist for old sliding doors on house remodels and re purposing the large panels of glass as a skylight over the top (heavy). Still looking for possible answers, not more information describing the problem, I know what it is.

Are you open to changing the roof design? A cupola built with your old windows as walls would let in a lot of light on top of a smooth roof. Add a weathervane on top to finish with style.

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Flex Seal Spray Rubber Sealant Coating

No windows will work unless you agree to build a curb on the roof.