Why don’t you post some information about the boat and pics of what we are working with? Your asking for help and all we know is you took some water in the bilge area and it’s got a Johnson pump. That’s not enough information to even start troubleshooting.
From what you’ve said though, silicon isn’t a very good sealant for what your trying to do. Sikaflex or 3M 4200 would be my suggestion.
I’ll also add. My bilge pump is a Johnson like this
It lives behind the bait pump back there
Before I put the water witch float on, it ran dry for hours. Probably hundreds of hours. It still works like a champ and doesn’t leak. It did pick up some fishing line in the impeller once and didn’t work very good but was easy enough to fix.