Nismo fuel pumps are only 275lph or something silly. Sure they bolt in but thats about it. 450lph walbro pump will also cost ~150 bucks less IIRC. If the R33gtst fuel pump mount setup is similar to the R32gtst it's a peice of piss to modify it to fit, though getting to the tank may be harder due to 33's being less likely to combust in a rear end accident.
You could probably easily go smaller injectors (720cc?) and shave off a hundred bucks. Also make sure you buy side feed injectors to suite your fuel rail, with the right size holes etc.
Really need a FPR? Making 300kw's here without one, but maybe there's different stuff on the GTR fuel system?
I wouldn't double the tuning, maybe add only 50%, for flex. You're basically getting two tunes in there. That's assuming you have no issues however, which can quickly add up unfortunately. I mean, best case, just a 98 tune, 500 bucks maybe. Worst case, things to wrong, flex tune, 2000 bucks isn't out of the question, so be ware.
you're also just missing little stuff. Turbo gaskets, new studs, fittings for Ethanol sensor and the like can add up to a few hundred bucks
You'll need to figure out how you're going to get the car to the tuner aswell, Everything you need to do is easy enough to DIY at home (and... satisfying to do, i'd recommend it), but with bigger injectors the car will be undrivable unless you can get the tune adjusted for the injectors. Not sure how easy haltec is to modify