My wife and I renovated our CJ this past summer and chief amongst the issues were windows
. What we did was:
1. Made sure the drain gaps at the bottom of the window track was open
2. Took all screws out and removed the windows
and cleaned and sanded gunk and rotted wood
3. Butyl taped window to body
4. Installed thicker window trim inside (most was rotted anyway) to allow for longer holding screws
5. Re-installed windows
with longer holding screws.
6. The crowning feature though was that we installed a 'splash guard' at the top of each window using the original screw holes. These I 'manufactured' from a strip of aluminum 90 angle roof edge - 1 1/2" drip run slightly bent down for drainage. We sealed the top raw edge with sealant. The feature extends 1 1/2 inches out from each side of the windows and the edge was rolled down slightly.
We encountered 2 major rains this past summer. The splash guard redirected the water and caused less to accumulate in the bottom rail of the window.
Good luck fellow Compact owner. We rule.<_<