I think we have a fix. We tried using the outside flaps, bought two different ladders to put them up/down with. Was totally turned off by having to either:
1) Play it safe and close the outside flaps before bed - just in case it rains. ESPECIALLY so when it is HOT outside and a thunderstorm is going to come through for sure at night.
2) Run outside and deploy (even if it is just to roll them down) in a powerful rain storm. No fun...
3) I was about to use Turbocity Tom's method from this thread and decided to try one more time...
We had already sealed all the seams, which helped a lot. Now at least the stitching didn't leak. Water still pooled and run along the bottom and dripped out the ends though.
So, with a container of HH-66 Vinyl Cement in hand, and my wife ready to help do some stitching, we set about to create a "dam" that would stop the water making it to either end.
I applied HH-66 to about 3/4" of the bottom end of the Velcro that attaches the clear plastic part of the window, making sure to get some into the very bottom of the gutter too so water can't sneak in under the seal/dam we are making.
Then, with one of us outside the camper and the other inside, we applied 6-7 stitches (most of them double, ends quadruple) to hold the glued Velcro bits together. Let it cure and test...
Tada! Water runs down the gutter between the mesh and the clear plastic, and now encounters a tight seal before the end of the gutter where we stitched/glued it. The water builds up high enough (not 3/4" though) to then run out of the mesh rather than find an easier escape inside the camper.
We tested all 4 windows with a garden hose on pretty high pressure and no leaks. If it leaks now, it will be because rain pushes sideways hard enough to penetrate the velcro way up on the sides of the windows.
We're keeping the outside flaps rolled up for now. Supposed to be a thunderstorm tonight, and instead of making sure the camper is locked up tight, we're going to leave it popped up to test the new windows again in real weather.