Nowadays all modern diesels vehicles are sold with turbochargers. This is not because it is cheaper to produce, but because the market and emissions requirements dictate that it must be so.
Similarly it is with intercoolers, where initially turbo diesels were not intercooled from the factory. Due to the obvious benefits of intercooling, the first models had top mounted intercoolers as that was the easiest to install on the production line where the intercooler is part of the engine package that was bolted into the chassis with the rest of the drivetrain and then the body was installed.
As is the case with performance street cars, the intercooler was moved to the front for optimum benefits. This can be seen in the 3L D4D powered Prado where the 150 series (front mounted intercooler) has better onroad power and torque over the previous 120 series with its top mounted intercooler.
Adding a top mount intercooler or increasing the size of your top mount intercooler will make a noticeable improvement.
Changing to a front mount installation is the next logical step. In the same conditions the inlet air temp can be expected to be 20-150deg cooler with a top mounted intercooler, which equates to more than 20-40% more air and therefore power potential.