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...
I Put a Aftermarket double din in my 4runner and used a special harness to keep the stock amp in the mix. I would love to get a better amp in there but between that and replacing all those speakers it would get expensive quick so I just decided to buy the harness for now and maybe down the road...