Drain hole cleaning methods?

I also had a bad passenger side leak. Turned out it was not coming from inside the cowl area, but water, doing what water will do, was coming in somehow from the area under the hood where all the pieces of sheet metal make a sandwich. I think through surface tension, it was going down, and then back up under the ledge where a lot of people mount the electronic ignition module. I ended up sealing up under that lip, and the leak went away.

Sounds familiar. I dug out as much of the old sealant as i could all the way across under that seam. Then resealed with neoprene roof caulk. That was actually ( at least so far) the final step in a long clean out and leak finding ordeal. Before that were leaks in the windshield gasket and holes in the corners of the metal, wiper pivots. Rust pinholes around the hole to the heater box. One that really had me for a while was right under the cowl drain hole. The flange you could see was fine, but the lower part was rusted away, so the water pouring out of the hole went right into the car.

As for the original clean out question... Before i did all that leak stop stuff,- I first tried wire in the drain holes (fenders off) while flushing water from above. Found there was too much to fit through the drains. Let it all dry out. Ran a small vacuum hose up through the heater box hole working it all the way across and sucked out as much as possible. Then used air hose from every angle possible to stir things up and vacuumed again. Repeated that several times.. When i had most of it cleared i went back to water flushing, blasting through every hole at every angle possible till no more crap came out.