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Not sure what you mean by intake holes. If you mean the holes under the flushing rim of the bowl then try a wire coat hanger and poke it into the holes.
The problem is that nothing will stay put up under the rim long enough to work. You dump the products you've tried into the flush valve at the bottom of the tank while you hold the flapper up. Have you tried this? You can't use a stronger acid it will stain/ruin the finish on the bowl. You're only other option is to carefully chip away at it.