I have fitted an intercooler and other things that muck about with fuel air ratio which leaves me to guestimate how much to turn up the fuel . Basically i have set the fuel at the pump to run as rich as possible without producing clouds of black smoke on start up and the truck runs fine , but i feel it could be better , it feels to me like she runs rich in the low rev range while getting lean further up the scale .
Shayne, that's the problem with adjusting the fuel at the actual pump. At low speeds and revs you don't actually need that much fuel as you're on constant boost already, but as you increase the revs you supply more fuel but proportionally not much of a increase in air, hence why you may be leaner on the top side and richer on the bottom. I don't think there's anything wrong with running a little rich on a Diesel, you may get slightly higher EGT but it would be small I imagine.
Regarding the throttle plate removal, it seems pretty popular on the Australian forum. I was going to do this at some point as well, I believe it'll increase the air flow a lot throughout the rev range and overall supply more air to the engine without the awkward restriction in place! Only downside I've read is you get a slightly rough shut down as the engine comes to a hault, I imagine this is because it's still getting plentiful supply of air but no fuel. Another con, is the possibility of a run away engine, but I think I'm getting ahead of myself here. Some guys have done the mod and have noticed no change in shutting down...
I reckon the next step you want to be looking at Shayne, is getting the max boost out of your Turbo, safely of course! Maybe nows a good time to use a bleed control valve on the waste gate line and up the boost a little. I would recommend you put a Boost guage in first. Being that you have a really good Exhaust system, I reckon you'll be fine on the heat side of things.
And also I like the intercooler setup but when I do mine, I think I'll fabricate the IC pipe to join at the side of the intake manifold as I've heard on the standard top intake it jams air down cyclinders 3 and 4 and leaves 1 and 2 struggling a little. You can kinda see this when looking at the intake...