DVM is right guy's !!!. I know its a lot of work but your talking about a structural component here and if you intend for it to hold up at all, replace it.
Patching is fine but you cant patch a frame rail properly near the shakles unless you remove the trunk pan. If your going to do that, replace the thing and be done with it. You are only postponing the inevitable.
Remember, hind sight is 20 - 20 and we have all been in a position when we wished we had done something differently.
'66 Ragtop, vibrant red, 289-4V, 4-speed toploader
'68 Fastback, space blue metalic, 351C-4-V, 4-speed toploader
'69 Mach I, (Pending Resto Project)
'66 Fastback (because I wanted one)