Similar Basement Seep Question

We had 5" of rain, and near one corner of my house with all in-ground basement, there is a window with outside window well, with stones at the bottom. Just to the left of the edge of the window well in the basement is a penetration into the basement of the lines from the outdoor A/C. Just under that there was a little seepage, which ran in a vertical line a couple of feet down the basement wall, then stopped. The basement wall is poured concrete.
What is the best approach to prevent a recurrence? Should I cover the window well with a plastic bubble cover? I have an oil tank in the basement and the lines for the oil are too close to the window well to install a standard plastic bubble, and I also have an electric line to attach a gas-powered generator to an electric panel in the basement, that also blocks a standard plastic window bubble cover.
What about caulk under the A/C line penetration in the basement, or dry-lok paint? Any other ideas?
Finally, what does it mean that the wet area on the basement wall still is visible days after the rain stopped?
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The best waterproofing is always done from the outside. Pipe penetrations are hard to seal when done right, I imagine they have two lines coming through one hole - it would have been easier to work with two holes with one line. Dig it up on the outside, be careful around the copper line set, Get generous with the hole so you can really clean the wall where the lines are going through. Use plastic roof cement and reinforcing cloth, be generous and thorough, and cover the fresh tar with a shield of card board, Styrofoam, or other sheathing to keep the dirt from rubbing through the tar when you put it back in. Leave the protector board.
The dark color under the line set says the concrete is still saturated. You might also look up Xypex.
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I'd add that some type of window well cover is also a good idea. Even if it's not complete because of the oil line, etc, covering up say 90% will keep a considerable amount of water out.

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