Can you post a picture of the area in question?
If it's where I think you're describing, razorblade off all the gobbed-up silicone back down to the gelcoat and see what's what there. Once the silicone's off and if the holes are reasonably round you can snap in white grommets.
Somebody in the past enlarged the drain holes, perhaps crudely, and tried (and failed) to "dress 'em up" with the silicone. Those holes on my '72 170 are only about 1/2" diameter.