Does the drain under the battery actually drain? Just because it's clear on top desn't mean the whole drain pipe is clear. Make sure it's draining rapidly otherwise water is still pooling up under there. Also, IIRC there are actually two drains. One is directly below the battery and another is up a bit higher, closer to the fender. The whole area under the battery should drain rapidly when you flood it. I wouldn't waste your time plugging the areas in the footwell that are leaking, the water will just find another place to leak out. I agree with the others that you are on the right track using the hose to find where the water is entering.

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LRG
1987 300D Turbo 175K
2006 Toyota Prius, efficent but no soul
1985 300 TDT(130K miles of trouble free motoring)now sold