The AEM EMS will do up to 2 channels of VVTi so a 1UZ with VVTi on the two intake cams should be no sweat.
The AEM EMS can be setup to work with the late model Toyota 36-2 crank trigger wheel that is found on the VVTi motors although a pull down resistor inside the ECU usually has to be changed to a 4K7 from a 2K2 to make it work. I did one a couple weeks ago actually, it was a turbo'd BEAMS 3S-GE engine in a Scion tC.
I have setup calibrations for the VVTi on the 1JZ & 2JZ motors in the past for people with good results (just ask Arnout) so a 1UZ shouldn't be that much different one would think.
I've tuned many VQ35DE's and EJ25's with intake cam timing control on both banks. Most notably a certain yellow (actually black now) 350Z. It's not something you want to leave unplugged as it usually adds quite a bit of low end power. On a VQ35DE engine, advancing the cams in the lower revs is good for about 80-100 ft-lbs. vs. leaving them in the default retarded position.
For reference,
VQ35DE's have ~41 degrees of adjustment
EJ25's have ~50 degrees of adjustment
1UZ's have ????? degrees of adjustment - anyone know???
Also, do you know if the VVTi 1UZ has 4-1 cam trigger wheels like most of the other Toyotas???
-MP