Finally found source of a leak I have been trying to track down for a while now. Turns out the livewell pump had a crack in the threaded part that goes thru the hull. I am gonna buy a new livewell pump and I am thinking about replaceing the bilge pump as well since the boat is almost 20 years old and both pumps are original. The wood in the transom appears to be ok but it did get wet. The boat is aluminum. Should I use 3m 5200 to seal the thru hull fitting or would I be ok with a silicone based sealer?

Thanks in advance

I'd use silicone.

Use marine grade silicone. Put a good bead on the flange of the through hull fitting, then tighten until you see it start to ooze around the edges of the flange. Let it sit for 24 hours, then tighten it. The silicone should set within 24 hours, making a nearly indestructible silicone gasket which when tightened makes an excellent watertight assembly. Do the same with the nut that goes on the threads.

The one concern is the wet wood. Is it exposed, so it can dry out after the fitting is installed? If not, you may have a problem. It would take months for the plywood to dry with the fitting removed. You could try some heat on the transom to force the moisture out. A halogen work light, at a safe distance would heat the transom around the hole quite well. Don't put it too close. Get the transom so it's just hot enough so you can leave your hand on it for a few seconds before it gets uncomfortable. A few hours of heating might drive out the moisture. It depends on how deeply it wicked into the wood. If you do this, do it outdoors away from buildings. Just in case.

While I am a great devotee of 3M 5200, I don't recommend it for this type of job. The stuff is nearly indestructible, and should you need to remove the fitting for any reason, you'll have to cut and grind it off.

I followed Rhino's advice for the same job and it worked out great

Replacing both is a good idea, and having one replacement motor assembly that will work on either one is also a good thing. Good luck.