I don't have a recommendation on the tuner shop, but I believe that a reasonable amount of additional power is attainable with the 1kz-te using the correct modifications. The 1kz-te can indeed take a lot more pressure because it was was not born as a naturally aspirated engine. The block, crank, and the bottom end as a whole were designed robustly and can handle significant boost.
The 1kz-te's shortcomings and performance bottlenecks (and by extension, many other Toyota/JDMs diesels) are steming from stock-oriented heat management and tolerance at the head, indirect injection performance penalties, one intake/exhaust valve setup. Limited room for timing tuneability. And horrid intake/exhaust manifolds geometry.
With that being said I personally believe that by using the following combination (not in order) a significant performance increase can be had with good reliability:
1. Manual transmission spec radiator (without integrated AT cooler, and a coolant temp sensor.
2. A dedicated transmission cooler.
3. 10 blade fan or high quality/performance brushless shrouded electric fan.
4. Auxillary external oil cooler with filter relocation.
5. A slightly overkill liquid/air intercooler with an adequate single core double pass radiator.
6. OE electric controlled fuel injection pump with a daisy chained chip such as Unichip. Boost controller.
7. Ported head, correct geometry intake runners, velocity stacks, plenum with EGR/throttle body delete in design, equal length exhaust headers with a pyrometer, and a turbo-back 3" exhaust.
These items combined can get expensive, not so much if you can fabricate. The Unichip might be the single most expensive item as the rest are affordable/fabricatable.
I have a KZJ78 with the 1kz-te and this is my recipe for the upcoming period.
Best of luck!!