I did this swap on my 2004 6 cyl

Just wannted to echo what other said the 5th gen rotors will work but produce a clicking noise which seems to come from play in the rotor because the holes where the lugnuts go are slightly to big. Rode my 4runner with 5th gen rotors for 2 years before noticing super uneven wear on one sides pads and not the other. Also noticed binding when lug nuts were tight, not sure why this wasnt an issue till later. Also we removed the rotors without using the star so had to rebuild the ebrakes for both side. So

TLDR
1. 5TH gen rotors work but are not ideal use 4th gen rotors
2. If you have clicking when in reverse you bent your ebrake hardware. (Specificly the _n_ shaped pin and lower spring behind the star nut adjuster.) Dont do it.

Thanks for the help guys, glad I can put some advice back in.