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This is a long read, but has pics .

Last summer I started noticing a musty smell in the car's cabin that dissipated after I started driving. I ruled out food or spilled liquids or drinks.
I checked the cabin filters and changed them.

I popped up the access panels on the windshield cowl and looked for debris or clogged drainage channels. There were none, so I flushed that area with water to be on the safe side. While doing that, I sprayed some Lysol in the A/C intake to let it circulate through the vents.
Yet the smell persisted. No chemical leaks, or animal nests, nothing I could detect. I felt and looked all through the cabin and trunk to check for leaks and found nothing. The car is always kept clean anyway, so I had to rule everything out.

After a thorough car detailing, the smell returned.
While vacuuming the cabin, I noticed a tiny bit of moisture on the underside of the driver's floor mat. Yet the carpet beneath was dry.
On a hunch, I pulled up the driver's floor carpet and found the carpet pad saturated with water.
It was only the driver's side, and I don't have a sunroof, so that's ruled out.

So where was it coming from? On another hunch, I popped open the driver's front wheel well shroud and took a look.
The hood release cable grommet was cracked. This is located directly under the windshield cowl's drainage channels, so every time it rained the water entered through the cracked boot and ran along until it reached the carpet padding.

The fix!
It reeeeeealy helps if you can avoid driving the car for a couple of days in very warm, dry weather, and can leave the windows down to aid in drying.
You need to get a replacement boot from Honda: "GROMMET, HOOD WIRE" Part Number: 74134-SH0-A01; Price: $0.92, and some clear silicone sealer.
If you need to replace the hood release cable anyway, this is the time for it, as the boot is included with it.

Take pics along the way if you need to.

Tools: Philips screwdrivers (1 long, 1 short), small flat blade driver, 10mm socket and ratchet, needle nose pliers, a chopstick, and towels.
Option: carpet cleaner extractor, spray bottle with water/bleach mix or Lysol spray.

Start the car, and turn the wheel as far left as you can get it.
To get the driver's carpet up, first remove the floor mats.
Pop up the driver's door sill trim piece (no tools needed).
Pop out the hood release trim piece, straight toward the gas and brake pedals (no tools needed).
Use a Philips to remove the trunk/fuel door release trim piece. It's tricky, as you need to adjust the key lock on it.
Remove the foot rest (10mm).
Pop out the round black plastic clip next to the gas pedal which attaches the carpet.

Once this is done, pull the carpet back. It's tricky getting it past the gas and brake pedals, but I found this very necessary.
Remove the underlying metal support beneath the footrest.
You can lay towels down to start soaking up the moisture (see pic 01; arrows show how water flows out).

Gently pull up the thin black foam/plastic barrier under the gas and brake pedals to look for moisture. Careful, as it's a bit fragile.
I put a towel beneath it and pushed down on it to drive the water onto the towel. Use small plastic lids to prop this piece up to speed drying.
If you follow the release cable up, you can feel where it goes behind this barrier and into the wheel well (see pic 02; arrows show how water flows behind barrier).
Use a carpet cleaner extractor (or wet/dry shop vac) to pull out the moisture from the insulation under the carpet.

This is what got me: the carpet has a tough, rubber bottom layer. Between that and the floorboard is the insulation. This is what was holding in that water, which caused the smell. Due to this rubber carpet backing, I couldn't detect the water. The carpet was still dry.
If you like, spray the carpet insulation with a water/bleach mix or Lysol spray to kill the mold and let it dry.

Remove the mudflap (Philips screwdrivers (1 long, 1 short)).
Remove the front wheel well shroud. You needn't remove it completely, just enough to bend it back to access the grommet.
Use the flat blade driver to pop up the center of the round black plastic clips, then use your fingers to pull both pieces out. There are only about 6 you need to remove (see pic 03).

Now you can see the grommet with the hood release cable running through it. It's probably cracked like mine was (see pic 04; arrows show cracks). Take a pic for future reference. The arrows indicate the flow of water from the drainage channels below the windshield. The flow goes right over that rubber boot (see pic 05). To be sure this is the source of your leak, pour a glass of water over the boot, and watch inside for water pooling onto your floorboard.

Next, remove the hood release bracket from the driver's side (10mm).
Use the pliers to unhook the cable from the hood release pull.

Tricky part: while in front of the wheel well, grab the release cable at the grommet and gently pull the end you just unhooked through it.
You may have to cut/break the old grommet, but it's fine.
Remove all traces of the old grommet from the hole it covered, and clean it off.
Notice how the cable end has a small barrel attached.
You have to gently work this end of the cable through the narrow end of the new grommet. Do it gently so it doesn't break. I sprayed some Armor-All in and out the grommet and that end of the cable to ease this step.

Now feed the cable back into the cabin through the hole and reattach it to the handle and bolt the mechanism back.
Open and close the hood a few times to make sure you have it correct.

Here's the hardest part: slide that new grommet into the hole without losing your cool. This is where the Armor-All came in handy, and the chopstick with a rounded end. Work the grommet into the hole with your fingers and chopstick in a clockwise motion until it's all seated. Start with the part that's hardest to reach, as it'll go in easiest.
You can feel with your fingers if you've done it properly.
Wipe off any dirt from the surrounding areas, and excess Armor-All.

Use the silicone sealer around the new grommet and where the cable exits it for a perfect seal.
You'll notice 2 other plugs in the firewall above the grommet, so you might as well run some sealer around those while you're at it (see pic 06).
Go ahead and put all the wheel well stuff back where it goes; you're done there.

Now all that's left is letting the car dry.
To speed things along, I got some DampRid and placed it in the car overnight for a few days to capture more moisture. I used the one that is on a small hanger, which I hung at the bottom of the driver's steering wheel. I placed a small plastic bin below that in case the bag leaked.
After a few days of drying out, you can safely place the carpet back down.
With all that done, I sprayed some carpet cleaning foam on the carpet and extracted it with the carpet cleaner.

After almost 5 months and several heavy rains, there is still no leak.

Note: I also have a '90 Accord and '05 Civic, and the boot is in a similar place on both of them. Anyone having floorboard leaks might want to check the rubber boot first as it's relatively easy to reach.
 

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