The W59 bellhousing that fits the 3RZ motor will not fit any of the R series transmissions. Marlin Crawler used to build a bellhousing to fit the 3RZ and R series, but I don't think you can get them any more.
You will need to find a G or W series transmission in order to use the W59 bellhousing.
You have to use the 3RZ clutch.
The 3RZ radiator hoses hook up to a 22R radiator.
I've made several stand alone wiring harnesses. It's pretty involved to do it correctly. If you are good at reading Toyota FSM wiring diagrams it's not that bad. Toyota wiring is a lot harder to stand alone than US engines. They bury the relays and fuses needed to run the engine into the dash harness. There's a mile of unneeded wiring to sort through to get the wires you need.
The ECM does not need to be tuned.
The automatic ECU's will work just fine. First swap I did, I used an auto ECU and it's got about 75K miles since the swap. It does throw a code for the shift solenoids, but does not affect the way it runs at all.
It's a little work to do the swap, but it's awesome for a Toyota motor.
Hope that helps.