Wow, the kids could almost go swimming in that! It must have been leaking a long time to accumulate that much. It's highly unlikely the boot for the wiring harness would be affected or even touched during the install but anythings possible. I would agree with lauj. Get some clear silicon in there and it should put an end to it. It's probably easier to seal it up from inside as you've got a better chance of forcing it in and having it squish out the firewall side while you have clear access under the dash. The engine bay side is too cramped and likely won't be able to get a good shot at pushing the silicone in from there.
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