if you're planning on putting on z32 calipers, do that first. as stated above, the larger calipers will actually increase your pedal travel and braking torque so the pedal will be more effective. you might find that it's ok with the stock booster. i have a z32 setup and 17/16 MC and a stock booster and the pedal feels great.
i see what you're saying about changing one part at a time, but the brakes are a system, dependant on all parts of the system to produce the desired result. kind of like putting stiff springs on stock shocks and being shocked that the suspension feels like shit. brakes are hardly new territory, you can do it all at once and be fine.
any idea what the piston diameter is on the 180sx calipers?
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