Different rating types (SAE vs. i forget) but yea no changes.

The big difference between the 04'/previous motor/tranny, it has been around since the 80's (the design) where they are still working out the bugs in the 04'+ (1gr was in a 4runner in 04)... and they are definately not as the 5vzfe... i think the 5vzfe was the last of the overbuilt truck motors by toyota, everything now is more "americanized".
If you're planning on keeping it stock, go with the 1gr (4 liter) modified? go 3.4, it will take more money to get the same power, but it will LAST... the 5vz bottom end stock has been pushed to over 400 hp, where the 1gr bottom end has been blowing up over 300 unless there is a very good tune... and the motors cost way more to replace.
The 1/4 mile speeds on the 1gr is around 15-mid 15 seconds, where the 5vzfe is high 16's low 17's.. so a huge speed difference, but the trd blower can make up for it.