I think you have a good plan, I agree as you suggested ........
1) Sand off all the old goop and clean it up nice ( a couple scratches will help bond the epoxy/goop/whatever you use )
2) I'd suggest using 3M 5200 marine sealant/adhesive on it. Although it does not specifically say aluminum - trust me that #$%^ will stick to it - no problem for years. Comes in black and white.
http://www.3m.com/product/informatio...e-Sealant.html
I had a piece of crap 12 foor tinner, bought for $75, that seen it's fair share of rocks, poor repairs, cracks and seam issues. I cleaned it up - pounded down the rivets and coated the boat with 5200 and she was bone dry - my cousin still runs the same boat some 15 years later and she is still nice and dry.
Looks like crap but it's dry. He is no Picaso and I'm hand tool challenged. We used a plastic putty knife to push it into the cracks and worked the product into all the seams and problem areas.