I've always used silicon grease for this type of duty. Silicon grease will not damage most rubbers, unlike petroleum greases. I've also got an old tub of red "rubber grease", used for assembling hydraulic systems here, but tend not to use that. I think it's vegetable based? It's often available cheaply in small sachets at motor factors.
On my boat, I've found that perseverance with a weepy bailer often pays off. I guess that it's often been a small foreign object (grit, weed or similar?) Often sorts itself out after a few days, and open/closed cycles. The leak then just stops. The sticky grease has the disadvantage of attracting this sort of debris.
Regarding the flooding, in the aft well. Do a few searches, there is a lot of very helpful info on here, I've pinched some of these ideas/experiences.
As my boat generally lives all season on a mid river swing mooring, I fill my ballast tank, burp it by going right forward, then force a medium size fender into the full ballast tank. I find this presses up the ballast tank, yet acts as a damper, rather like those in a hydraulic accumulator.
As it also displaces water, it will increase the freeboard, hence reduce the level of any flood water inside the moored boat, should the bailers be left open. Mine doesn't come above the lip of the sump, even with me inside the boat.
I've recently added copperbot anti foul to the sump, but otherwise the interior of the boat stays clean and dry.