Rust around the bed mounting bolts is a common issue with the Tundra!
It occurs from the BOTTOM UP. The seam sealer Toyota uses on the underside of the bed dries out over time, and allows water to creep in between the main bed crossbeams and the bed floor. The inherent vibrations around the bolt mounting areas draw the moisture deeply into the seams, and sets up rust.
On my 2008, I just completed a big project of cutting out large areas around the mounting bolts, replacing with .100" thick sheet metal, sealing, and then rolling on Herculiner (good stuff).
I don't weld flat sheet metal to sheet metal; instead I use Sika 291 marine adhesive to bond the panels, and for seam sealing/tapering afterwards.
When you weld-in patches, the thin sheet metal of the bed floor doesn't allow for very heavy welds, and even being welded, it's only attached around the edges of the patch metal. When you bond the patches with the thick Sika, they are attached to more surface area of the truck bed, and more importantly to the bed crossbeams below your cutouts.
Use new bed bolts! McMaster-Carr has the M12x1.25x110 (100 length also works), 5 pcs for the price of 1 Toyota bolt. Reuse the nice thick factory washers by grinding the OD of the bolts slightly.
ToolCat