As said by everyone else, well researched! A few things I'd note:
You will need a new pedal box, your cable clutch pedal box is different from the 98-01 Impreza 2.5 RS hydraulic pedal box.
I wouldn't worry about the master cylinder right away. Having the smaller non-ABS master cylinder will give a bit more pedal travel, but the Brembo brakes will still function and have bite. If you want a firmer pedal later, look into the master cylinder upgrade specified above.
However, I would make sure that you find a non-ABS rear disc brake proportioning valve. This will prevent your rear brakes from locking up before the fronts and give you a correct brake bias. Another option would be to replace your stock proportioning valve with a manually adjustable one.
As for control arms and lateral links: If you plan to go turbo eventually, swap the front subframe as well. You will not be able to run the GD STi control arms without this. As for which track width to use, it's up to you. The wider track width requires rear GD lateral links, a front GD subframe, and front GD control arms. If you're going to run STi sway bars, I'd recommend this route. Otherwise, you can run the front GD subframe, front GC control arms with shims, rear GC lateral links, and GC aftermarket sway bars.
Axle wise, I am running GD STi axles with the GC track width in the rear, and the axles are compressed a bit, but do function properly. It may generate a bit of rear end noise, but it's hard to tell, as I have Whiteline diff bushings and the subframe lockdown kit installed as well. GD track front and rear will free them up, but I would not run a GD track in one end with a GC track in the other.
Regarding subframes, they do not appreciably alter your track width, that is done by the lateral links in the rear and the control arms in front. Choose them based on condition in the rear (rusty vs. newer, etc) and your choice of control arm and motor (turbo yes or no) in the front.
The fuel tank is up to preference, although from what I understand the STi tank has better baffling and the pump arm is better suited for high speed cornering. While I've not performed the swap on any of my cars, if I had the opportunity to do so I would.