Ok, I fianally got some work done on this sloooooow moving project this weekend. I got the battery relocated, the '01 2rz wirring installed on the engine, the intake installed, the radiator installed, the fuel line finished, the dash torn apart, egr system removed, heater hose/valve setup done, and removed the connector for the ecu that I need from the dash wirring harness.
I found out that the '04 3rz has a egr system while the '01 2rz does not. So, since this will be smogged like a '01 2rz, I removed the egr system completely. This gives me a little more room to work behind the motor and cleans up the engine bay too.
I did find something out to my suprise though: the connectors for the knock sensor and the ignition switched positive wire for the starter are not included in the engine harness. It looks as if I will have to make my own harness on the left side of the engine bay to get things to work right. - Shouldn't be too bad, although I will have to run sheilded wire for the knock sensor. I hope coaxial cable will do the trick.