5200 is good stuff, but it is PERMANENT! I use silicone where possible, especially if there is any chance you will have to remove the part in the future.
Look at the hobie assembly manual and parts guide.
http://static.hobiecat.com/digital_assets/hc16_manual_gb_201503.pdf and
http://static.hobiecat.com/digital_assets/14-16Parts2016.pdfor click on the Support link at the top of the page.
They will show how things go together and which parts are correct.
Use your local Hobie dealer if you can, if not, Murrays is great.
Hopefully you have a sail repair\loft nearby. They can make solid repairs and at least around here, the cost is really fair. To do it yourself requires a big zag stitch power sewing machine.
Sometimes on the mast base you can just drill new holes and add rivets rather than cutting the mast down. Pop the bottom off and have a look.
I haven't yet seen paint that holds up anywhere near as well as Gel-coat. That said, it would probably be cheaper to find better hulls than to redo a whole boat.
I use a waterproof bag that I d-ring to the front of the tramp for storage.