I removed the cowl and the wiper motor and found some small holes rusted through just below the wiper motor.
It seems that water could just sit there and rust any repair I do currently. What is the best way to prevent this from rusting again?
Is there a drain that I am missing?

Thanks

I don’t know the best way to prevent rust. I read once that someone lined that area with some kind of oil or lubricant.

I think the design is “flush and dry” rocker panels. The water is supposed to flush down near the kick panels and drain from the rocker panels.

Its best to pull off the cowl panel and clean out all the leaves and debris that's trapped down the sides where it supposed to drain. There's no real way to stop rust once it starts eating metal. You really have to cgind or cut it away then prime and paint the area.