I've heard it said that 1MZ and 3MZ heads are almost the same except a oil galery. Also the ports for the water passages are slightly different shape. But the biggest difference is it is said that "3mz heads have more room around the valves".

I found some pics of the chambers and it does indeed appear that 3mz heads do have some "unshrouding work" that appears to be done around the intake valves. I don't really see it on the exhaust side but maybe it does. Is this what they are talking about? That the chamber is layed back slightly on the intake valves to allow more flow?

I've attached pics of the chambers.

1mz chamber

3mz chamber. Notice that around the intake valves appears to be more space. If a porter had laid back the chamber on a 1mz head with a ball cutter it would look similar.

 

The chamber on the 3mz cyllinder head is more of an "open" chamber design with the combustion chamber flatter and not as deep. The exhaust valves on the 3mz heads are not obstructed by the chamber wall like they are on the 1mz heads. So when they say the 3mz heads have more space around the valves than the 1mz heads, it's obvious in the pics and it's a big deal. It's going to help low lift flow especially, but it'll help flow over the entire curve. People when they get chamber work get this work done in the chamber to improve the flow. Toyota did it from the factory on the 3mz head.