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Assuming your holes are for wiring, use the tubing to prevent things from chafing on the cut edge, and wrap your wiring bundle in foam to bulk it up enough that it forms a seal against the tubing. Wrap that in plastic wiring loom to keep water out of the foam, and seal the ends with black tape or heat shrink. Looks terrible, but should get the job done.
For round holes, I've seen some rubber plugs here and there (can't name a supplier) that you can cut a small hole in and push the wiring bundle through, which would form an adequate seal.
Molding your own rubber parts would be idea. I've got an older book on molding your own rubber parts, but it was published in the UK, and the various trade names mentioned are unknown here.
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