5200 should have no effect on the tank...it is a widely used adhesive for gluing in the rubber strips.....just make sure its completely glued in, ie, no gaps or voids...the edges of the rubber should look like caulk around your bathtub.....
I don't know about gluing down the strip to the hull...most people secure the tank in 3 ways...one is the use of welded on angle brackets that are lagged to all 4 sides, into the long side stringers and the short side bulkheads....another is the use of wedge blocks, basically doing the same thing, 2 along the bulkheads and 3 along each length against the stringers and then screwed through the wedges and into the bulkhead and stringers..that was most likely the way the factory did it...you should glue rubber strips to the tank in these wedge areas to protect the tank from rubbing.....third is to foam in the tank, but the foam can't be the only means of securement....you must still use wedges or brackets...the tank cannot move more than a 1/4 inch in any direction, (I think thats the number) but you need to confirm that with Coast Guard regulations..it tells you what the maximum movement can be.
As far as piant or not to paint....paint itself won't do much at all....there are 2 frames of thought...one is to allow the bare aluminum to oxidize itself which leaves a protective coating of aluminum oxide on the surface...this is how it was left from the factory//probably give you 20 years of life..the key is to keep the coffin box as dry as possible....if moisture is a constant in the coffin, you will see the wet spots oxidfize much faster, leaving a white powder on the surface...these areas will pinhole through much quicker, shortening the life of the tank...especially around the welds
the second school of thought is to put a coating on the aluminum to barrier coat it from moisture all together....you have to first prep the aluminum by sanding and etching and then quickly drying before putting on a coat of either barrier coat epoxy such as Interprotect 2000 (at least 3 coats) or use the black nasty epoxy called coal tar epoxy...both are supposed to block moisture intrusion...but you have about an hour to get all 3 prep steps, ie sand, etch and first coat , before the aluminum begins to oxidize....the biggest issue with barrier coating failure is that if you scratch or damage the coating during installation, moisture will find that bad spot and slowly get in between the coating and the metal...once that starts, it keeps on going, trapping moisture in the bubbled areas....so you need to be careful...
a new way of coating it useing the Line-X truck bed liner....looks great and is very tough....but the jury is out on its long term effectiveness as I don't think anyone has 20 years of data to prove how well it works.....