How To Fix ATM's Boat

You may remember a while back I mentioned my front livewell came from the factory with a drain hole that no plug would fit. And that I was gonna take it to War Eagle for them to fix. What i haven't mentioned was that I have a aerator pump that fills the front livewell and baitwell. It hasn't worked right from day one. The longer I have the boat the worse it works.
I went by Counce Marine yesterday and they called War Eagle to schedule me for next Tuesday. While they had them on the phone they told them I wanted my front aerator pump changed out too. Come to find out War Eagle has been having trouble with these front aerator pumps. Seems that with the big heavy four strokes, 3 group 31's plus a starting battery, 4 bank chargers, etc. the backs of the boats are setting lower and the fronts higher. With the aerator pump being in the front of the boat and pulling from the front starboard side they are getting air lock. Makes a whole lot of sense to me. Their cure is to plumb a new pump into the rear of the boat. Sounds good so far.
On a related project. Occasionally I could get the aerator pump to work and fill the baitwell, which is a 3 gallon molded compartment with a 2 gallon perforated minner bucket. With the bow rising while getting on plane, when I got to where I was going I had a 3 gallon molded compartment with a 2 gallon perforated minner bucket, with about a gallon of water in it. 2 gallons of water would go out the overflow on acceleration. This left about 2" of water for all my minners.
Now, down to my questions:

1) The aerator pump is connected to a 1" dia. 6" long piece of aluminum welded in my hull. How should they patch that hole?

2) Even if the baitwell worked perfectly, which it doesn't, it would still be a sorry excuse for a minner bucket. Should I have them remove it and build be a liner for general storage?