Hmmm. Someone just posted yesterday how they would buy a Toyota because it has a C-channel frame, vs. a Ford/Chevy boxed frame. They were afraid a boxed frame would trap moisture and corrode.
Based on Toyotas current track record with frames they might want to re-think that statement. This recall has been out there for a while now.
When they do your frame swap, they will likely try to charge you for all the ancillary parts you mentioned. They will tell you that the shocks were completely worn out anyway, multiple fasteners etc. Make sure you hold them responsible.