Congrats on your new (and comfy) crusier!
I can comment on the following:
1kz has a limit to how much heat it can deal with. If you increase load/performance/duration under stress, you really need to increase cooling capacity.
Look at upgraded or rebuilt factory radiators, 10 blade fan, new/refilled viscous hub, GAUGES. (coolant temp/intake air temp/exhaust gas temp)
JRP Gauges (Diesel Kit Australia)
3" dump pipe and exhaust makes a huge improvement. The extra size allows for heat to be purged out at a much quicker rate than factory.
I had an off the shelf kit from PPD and it was pretty decent in my old vehicle. If I was to do it again (KZJ120 Prado) I would add an extra oval profile muffler with offset inlet/outlet for extra stealth and retaining maximum flow/heat dispersion.
You may be able to order a dump pipe and then get the rest of the system custom made
One intercooler setup I utilised removed the throttle butterfly, and was very quick, but the piping I used I would consider slightly oversized (2.75 inch)
I would stick to 2.5 inch max intercooler pipe.
3 inch max intake pipe.
I had a used intercooler from an XR6 turbo falcon, installed as a top mount, with a 12 inch thermo fan underneath (rigged to a temp controller and two speed relay system and speed controller) It automatically came on at a designated temp, then increased to high speed (like industrial sounding speed) under high boost or prolonged heat. This also helped purge the engine bay of excess heat when in traffic too.
Front mount is going to be simpler but can require a bit of cutting and long pipe routes.
Water to air setup would be worth looking into, if you can stand reading a 25 year old website:
ARE Cooling - https://www.are.com.au/feat/techt/airwaterinter.htm
They made a 1KZTE option back then, with data to back up the claims.
Tyre Size:
The retro cheese cutters look the part, but those extra inches in size are the difference between reaching 100km/h on the highway today, or some time later.
Hills and long 80km to 100km transitions up a gradient, you will feel right at home in the left lane. I would look at a 2nd set of alloys for daily duties. Even some mint 3 piece JDM period correct (SSR, BBS, Enekei,) with max 31" tyres (Kumho RoadVenture are awesome for the price)
The more involved mods involve turbo replacement, injector pump tweaking (Unichip X, or swap to mechanical) and actual injector replacements.
These options are serious $$$,
If you are really keen,,,, all of the above can be solved with a 1KDftv replacement. Nearly double the power and much better economy. Just fix the s*** injector issue which once sorted, a 1KD 78 series would be going up the hills at 150km/h if you wind it up. (plus you could run the retro wheels with ease)
THis level of conversion, may have been documented and done before here in Aus too