After 14 years of owning this Flex and parking outside, this problem finally hit me. Thanks @revidium (wherever you are) for the write-up and video tutorial! It plus the comments section made this job a snap.
My post isn't intended to be a tutorial, but a supplement to help the job go a little more smoothly.
For starters, my symptoms: my area had just experienced the first heavy rain of the season, but it was nothing extraordinary, not a "trees are down and roads are flooded" but more just a half day of steady rain. So no big deal.
But when I drove the Flex the next day, the ventilation fan sputtered ("spluttered") any my son noticed a bit of water flowing out of the footwell vent.
After finding this thread and the how-to video, I got to the plenum tray under the cowl cover and I found inches-deep standing water, even though it now hasn't rained for over a week.
Rather than poking at and vacuuming the clogged drain spouts like revidium demonstrates in his video, I just gave each on a gentle squeeze and lifted them out and gave them thorough cleanings.
The HVAC intake does in fact appear to be the scupper drain for this tray, right into the cabin filter box. The metal prefilter screen is in a very confined space. It looks delicate. The plastic box the screen is attached to looks as though it is adhesively attached / sealed to the sheetmetal, so there's no way I can see to easily remove it. Just light side-to-side finger pressure, coming in from the side, and I was able to rub most of the accumulated dust and hair off of the screen. No, a compact blower didn't work.
Lastly, the ECM and its wiring bundle also occupy this space. The corrosion on the chassis on mine makes it look as if it's been submerged, but that's doubtful, because the unit sits higher than the HVAC intake. In theory standing water shouldn't be able to reach it.