This is a sad statement
"But with a 2 year warranty for 3000, it seems like a decent deal if I can get at least 2-4 years out of the motor."
A properly rebuilt 1FZ-FE should go for way more than 2-4 years.
You want to swap engines and then have the old one as spare parts. This is Land Rover/Jeep mentality. You shouldn't need parts from the old engine if the rebuilt was done to spec in the first place. Get where I'm coming from?
"my old engine is shot" - do you know if the lower end is shot too? The lower end is quite robust so you maybe able to get away with very minimal honing, new rings and bearings. Just talking out loud here.
As far as the ECU harness, dump the old one and buy a new one. These harnesses are becoming crispy critters and this type of major disturbance really messes with the connections and not worth taking the risk IMHO. Imagine how PO'ed you'd be after the new/rebuilt engine goes in, you then fight weird gremlins.
Yes, it is easier to pull the engine/trans/transfer case combo out with the ECU harness intact, just disconnect it from the ECU. See pic.
My advice, for what that's worth, is to pull the old engine out, take it apart, rebuild it with OEM parts then stick it back in. Your'e good to go for another 20 years.