Mixing toyota coolant with regular coolant wreaks havoc with the anti corrosive agents in the coolant (they cancel each other out or something) so that could be what caused the rust in the first place.

You're there. Only you can tell if it's rust or not. We can't

Might just be Red coolant mixed with Green or Yellow to give that colour.

If you check it with an antifreeze tester and if it is indeed antifreeze then it's probably not rust.

Drain it. Flush it. See what happens.

so we replaced the thermostat, drained radiator, filled with new coolant and the leaking stopped. But when we started it, it started to overheat. what could we have done wrong or what could have happened?

Air in the system. You need to burp the system.

Jack up the truck so the nose is up high then i forget what else to do. lol sorry.

air bubble in system
burb system however you wish
jack up front end to move air bubbles to higher ground
squeeze hoses
leave rad cap off ................................................

Let it cool, remove the cap and squeeze the upper hose, do this a few times then start it and repeat, adding coolant as you go. when it starts to warm up, put the cap on loose go for a short ride (less than a mile) and let it cool...remove the cap and start over...squeeze the top hose a few times adding coolant, etc...