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Pics would help, particularly of the cracks. It depends on how deep/where they are as to whether they're an issue.
Regarding the trunks, you'd keep them down while going along in rough weather so any water that comes in would go straight out again. They get rid of huge volumes of water very fast, so if you get a wave into the boat they'll be invaluable. I emptied my SR5.4 from a full stuff, water level with transom in under a minute using mine.
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