They should replace it for free, but before that make sure they give you a receipt for what they want to do. You don’t want to pay for extra stuff that you don’t need. 

Don’t have answer, but in similar situation with rusted frame and believe more input better than none. I too was recently approved for Tundra rusted frame replacement (2001 SR5, V8 TRD, 300k miles). I had front end redone several years ago, engine runs strong and tranny seems good shape. When I expressed my concern about understanding price of items NOT covered under warranty (this in an attempt to understand ancillary costs and avoid getting meat hooks put into me AFTER the truck is tore down (bad place to be)) the dealership offered to do an assessment of items probably requiring replacement that are NOT covered under Toyota Corporate (items that might break or not properly go back together: rusted bolts, brackets, muffler system, etc.) based on knowledge from the many other frame replacement jobs they’ve done. I can understand that some stuff too far gone to disassemble without damage and/or cannot be properly reassembled. Few weeks later when I called to schedule the assessment (I’m not an impulse decision maker) the same customer service rep stated there a fee for the assessment (an hour at ~$120/hr). I asked why mention of assessment fee not initially stated and the service rep backpeddled that it was repair shop manager doing and tried the “I’m just the middle-person” response. I expressed that I would have appreciated initially knowing there would be a fee, how this doesn’t seem like good service (I realize it an old truck), it seems we off to not so good a communication start and could not the shop absorb this under the circumstances? No go. I will say I did get a bit “to the point” on the phone, but not rude or unprofessional. I called a different dealership - politely, concisely and Professionally explained my situation and then asked if they had interest in doing the work. They said sure. Now, there’s another hiccup I need to resolve. Seems the first dealership put order into Corporate for the new frame, despite me NOT not giving the go-ahead (no uncertain terms, I clearly stated I need to weigh my options (realizing age of truck and fact that I’m not an impulse decision maker)). Since first dealership entered order, the second dealership cannot duplicate (frame tied to VIN). Gotta get first dealership to release frame order placement or transfer over to second dealership. Left two messages with original dealership service rep without response. Figure I’ll need to visit original dealership to resolve. That’s where I stand right now. What a pain, but I love my Tundra.