The holes in the tray aren't a problem, it's where the tray attaches to the firewall. If there is rust there, you most likely have water entering there.

I would look under the battery tray first, then use a garden hose to track down the entry point of the water. No need to go through the effort of sealing the windshield if that isn't the problem.

__________________
Chad
2006 Nissan Pathfinder LE
1998 Acura 3.0 CL
OBK#44
"Pleasure in the job puts perfection in the work." - Aristotle (384-322 B.C.)

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1985 300TD - Red Dragon
1986 300SDL - Coda
1991 - 300TE
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1985 300CD - Gladys