For the OP - you should just weld this structure and skip the stainless fastners altogether.
If you need pins to hold it while fitting or trying, you can easily get marine
grade rod (threaded or not) any diameter. If threaded, cut a slot in the end for a flat screw driver. They will hold just fine with no corrosion
concern. And just weld them flush when you get it sorted/fitted/trailed.
The "stainless with goop" is just not the best solution.
If there are parts
that just have to be adjustable or removable, then go with either the #2 or #3 options I mentioned above, or if designed so the pins are not highly loaded the aluminum
rod would again work
well (with just a bit of design cleverness).