5200 is the one thing that's perfect for this. If you must use Sikflex, either because your family owns stock in the company or you're one of those people who insisted all through the 1990s that Windows was faster than a Mac, make sure you get the kind that is meant to go with aluminum. It's not the chemical adhesion that matters; it's the compound's ability to move when the aluminum moves with temperature changes. 5200 is made for this (Boeing airliners used it to hold windows in-- no screws-- just 5200).
Be very careful in backing toerail bolts out. I would do a smallish section at a time; also I would consider just rocking the thing up a little, using hard-plastic wedges and leaving the nuts on the bottoms of the bolts (where possible) and just squeezing the stuff underneath. Once the rail comes off, good luck putting it back.
Also I would strongly recommend replacing all the bolts. If you cannot get, or choose to not use, SS carriage bolts (what was original), then consider hex-heads. These, like carriage bolts, are easy for one person to use because you don't have to be topside to hold the head. With hex-heads, just get about 5 little 7/16"; wrenches and drop them onto the heads, then go below and crank up with your ratchet. The wrenches will stop against the rail and you'll be able to turn to your heart's content. One last yank on the wrenches from topside will free them to let them be removed-- and that's about exactly the amount of torque that the 5200 will need or allow.
Remember also to use Delrin flat washers under hex-head screws; with carriage bolts lube them well with Tef-Gel or something similar to minimize bimetallic corrosion.