RS Dude hit it on the head. It's fairly common. Many upgrade the front brakes to the last gen Tundra front brakes with success. I am not a 3rd gen guy and don't know if that will work with 16" wheels but some searching will reveal the answer.
Brake rotor brand is huge IMHO. Be it a Tundra upgrade or just OE brakes high quality rotors is key. One of my favs is the Napa Premium series for an OE replacement. You would think "rotors is rotors" but they aren't. Be careful of cheapy Ebay drilled/slotted too, some are good, some aren't.
Drilled is a whole other thing too, many in the know agree slotted is good but unless there's a substantial oversize put in place drilled isn't "all that".
My advice is to try again with some premium Napa, Brembo or other high quality rotor and ceramic pads.
:cheers: