David, the differences I found are:
The cylinder bore size has increased, of course, from 87.5 to 91.0mm, and the bores of the cylinder head gaskets have increased also, so you'd have to use the 3UZ head gaskets.
The water jackets in the heads have been changed to improve the flow around the valve seats and reduce the combustion chamber temperature. Don't know if this was in part due to the bore increase or ???
TIS states that the pitch of the 3UZ camshafts has been shortened and the valve angle has been "narrowed" to 21 degrees 33 minutes. I could find no specs for the valve angle of the 1UZ VVTi.
Intake valve timing has changed a bit, but this is a function of the VVTi controller. Valve sizes are the same as the 1UZ VVTi.
Cylinder head bolt material has changed and a higher clamping torque has been specified. (Perhaps this is related to the decrease in sealing surface between cylinders and the water jackets due to the increased bores?)
Looks to me like 3UZ heads might work on the 1UZ VVTi motor, and vice versa, but you'd want to check closely for good sealing of water jackets and between cylinders. If you did do a head interchange, it looks like it would have to be with the cams too. It doesn't appear that the 3UZ VVTi and 1UZ VVTi cams are interchangeable, however that's just my "read" of the TIS. Don't know how well manifolding and other ancillaries would bolt up.....
