Aydan,
I'm assuming your rebuilding your engine for more strength. If so, do the head bolts, and head gasket. I'm sure you're already aware of the 11 mm Raceware (and possibly ARP from techtonics tuning) fasteners that are available. I don't know of a source for metal head gaskets for the 76.5 mm bore/mechanical lifter heads though. zsimports.com sells 1, 2, or 3 notch "diesel/turbo diesel" head gaskets for 11 or 12 mm head bolt solid-lifter engines. I'm guessing these are better than the original head gaskets that came on our 1.5 L engines. I'm not sure how feasible it is to modify a 1.9 gasket. Between the coolant passages, oil passages and the fact that the 1.9 had a much larger bore, I think there may be too many differences.
I think newer/bigger injector nozzles are a good idea for several reasons. First, you'll need a bigger nozzle to inject more fuel in the already small injection window. Smaller injectors will cause fuel to be injected well into the power stroke, which will result in unburned fuel (lost HP and black smoke), and higher EGTs. After installing the larger nozzles, have the injectors pop-tested and adjust the breaking pressure to be at least as high as the TDs. As I understand it, the breaking pressures needs to be higher to help offset the higher dynamic compression ratio of the boosted engine. This will help ensure that there's enough differential between the injection pressure and the cylinder pressure to quickly inject, and fully atomize the fuel.
I would personally be in favor of a clutched SC, although I have no idea what it would take to implement a system like that.
As far as what boost to run, I have the same delimma. Since my turbo won't be wastegated (VNT), I'm kind of at the mercy of its open nozzle boost characteristics (which I'm hoping is around 15 lbs.) From there it can only go up. I'm not too worried about how to limit how much boost it has initially. They say to lower your EGTs, add more boost. What I am worried about is fueling and how much heat it will add when I start to go with significantly more fuel than stock.