The 2UZFE stock ECU runs the engine without the auto slush box attached. It will store codes due to missing signals from the transmission, but the engine still runs properly.
It has been a while since I buried my head in this, but if I recall what it won't do is start if it doesn't get the appropriate signal to indicate that the transmission is in park or neutral. The ECU also limits max rpm (to 4000 rpm IIRC) if it is running with the "missing transmission" in neutral or park.
This shouldn't require rocket science, piggyback ECUs or other gadgets to overcome, you should just have to supply the ECU with the appropriate 12v signal for "park/neutral" and "drive" positions etc.
From what I remember there were added complexities with the later 2UZFE VVTi (2007 and up - again IIRC), because of the VVTi, and its electronic chip key. The ECU needs the signal from that key otherwise the ECU won't allow the engine to crank. I don't remember what the complexity was with the VVTi specifically, perhaps there wasn't one, or maybe it was just the immobilizer key/ECU combo, but reading about other 2UZFE swaps I seem to think it made life more difficult.
I made sure that I got the ECU, harness, throttle cable and all bits and pieces I wanted from the guy who was parting out the donor truck.
There have been quite a few 2UZFE swaps done, most using the automatic, but plenty without. These guys are doing 1UZ/2UZ swaps in manual transmission 4Runners and other Toyotas. They have on the shelf parts to do these conversions, motor mounts, transmission adapter plates etc. but nothing specific to Cruisers unfortunately...
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