The standard brakes are fine with the right pads.
What are you talking about??? The standard brakes are rubbish with any pad, and I've tried them all.
Nissan would have put the Sunny Diesel brakes on because of cost, the same with the 14s. You can go on about 'Rally Theories' all you want but show me one rally 'R with standard wheels and brakes. The thing with cars like the 'R, Escort Cosworths, Integrales, is that they cost HUGE amounts to build and develop but the manufacturers know they will only break even if they are lucky on the costs (but that's not the point, it's the marketting kudos the manufacturers get from having a successful competition car that makes back the money). So to make sure they don't lose too much money, or upset the bean counters in the accounts department they would have HAD to build the car to a cost. With this limited budget they'd much rather spend it developing mechanical valve gear than spend it on a decent set of calipers and wheels, which would just be junked on the NME rally car anyway.
As for the gearbox, it isn't chocolate really, there are a few 'Rs around running 350 bhp on standard 'boxes and haven't broken them (I blame paddle clutches for the bad reputation myself). The thing with these are Nissan already have to build to a budget, so they're not going to waste money testing the 'box upto and beyond 400 bhp, just in case some mad modder wants to up the boost on his new Nissan. Again the NME cars wouldn't use the standard box, so Nissan would have just built a 'box that can cope with standard power and lets face it, a standard car will not break it's 'box unless you're doing something very stupid.
Finally, the GTi-R shell is not GTi-R specific, it's just 4WD specific and there are other 4WD Sunny/Pulsars about (1.6 petrol etc.). Again this is a cost thing, they would need to make back some money on the HUGE tooling costs required to build a one-off shell for a car they were only planning to build 5000 of. If it was GTi-R specific I would hedge my bets that they would have built a shell slightly more rigid than the cardboard attempt we all drive (the standard 'R shell is ridiculously flexible, hence why the cars react so well to a a few carefully chosen strut braces).
The road car is ALL about building to a cost, and nearly every 'weakpoint' on the road car is exactly where the standard part would find it's way to the bin before the rally car clocked it's first mile.