Thought Baring flood or accident damage ECMs in USA should be covered by a 8 year 80K emission warranty. Did you think to have Toyota run the  VIN # for ECM warranty coverage?  

 Yeah that ECM should be covered unless this is a salvage/rebuilt/flood and the dealer won't touch it. Reprogram will have to be through Toyota Techstream ($55 for 2 days access) and the MaxiFlash J2534 device. 

   yes it used to be covered under emissions warranty even if they were salvaged/rebuilt/flood tittles, I know cause I had more than a few covered  in the early and  mids 2000, then something changed and they started to void warranties , most dealers and independent shops wont even touch them now a days, specially flood damaged. we have a new one now also lightning strikes damaged, making them salvage tittles on some high end vehicles probably for the amount of modules that need to be replaced.