Have you looked at the bottoms of the doors themselves...there should be drain holes within metal areas.
Doors are designed to take on water from outside of door glass, then drain through door itself.
Is the flexible soft plastic weather shield (moisture vapor barrier) behind door panels/in front of door sheetmetal still in place ?
I am not sure what you mean by 'window seal retainer' ?
If I'm not spot on with above, you are welcome to send me a private message.
For what it's worth, the attached technical service bulletin TSB 08-26-7 has helped many of us diagnose water leaks on this body:
Last edited by s197gt; 02-22-2020 at 07:07 PM.