Nice work Jarrat! You're going to town on that thing! I'm stoked to see other guys in BC having fun with Prados.
Couple comments on your turbo. A couple times now I thought I'd reached the limit of the boost ability of my turbo. Then I turned the fuel up a bit more, and it made more boost! Basically it takes a certain amount of exhaust pressure/energy through the turbine to do a given amount of work at the compressor. With a diesel adding more fuel means more exhaust which in turn makes more boost. Now without an intercooler, you can't really turn up the fuel much, but once you have that intercooler in you can (lower EGTs from more dense air). I found I get about 16psi max with the fuel pump turned right up (intercooled). When my methanol injection comes on (adding more fuel), I can get 18psi max. So in a nutshell, your old turbo might be just fine. Try out your new one before paying to have the old one rebuilt. Other things that help the turbo are free flowing air filters (like your K&N) and minimal exhaust back pressure. You've already addressed those things. I've come to realize these turbos are a bit on the big size for these motors, which at the end of the day means there is a lot of power potential over OEM.
And some advice for your intercooler (based on my experience). Don't mount your water pump up high like I did!! Mine was very prone to cavitation and was a real PITA to get the air out. If I did it again I'd mount the water pump down low in the front of the truck by the intercooler radiator. Also, make sure you can get all the air out of the intercooler and the intercooler radiator. If you don't you will be killing the efficiency. For example, put at least one hose connection up on your intercooler radiator, and this way the air will travel out of it and up higher in the system where you can get it out. The intercooler is more tricky to get the air out of. You can stand it up on end to bleed it, and then mount it once you have all the air out. Make sure your fill point is the highest point in the system. Finally, if you have a fan around, mount it on that little intercooler radiator until you get a bigger one. I think even in winter if you do a long drive, you could end up heat soaking your intercooler system (water will get real hot). It is possible even for it to boil under extreme conditions. Some guys plumb in a rad cap style pressure relief, because if the water gets too hot and there is too much pressure it could wreck the inside of your intercooler (blow the core up like a balloon and maybe even leak).
Keep up the good work!