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Garrett, excellent quality, reliability and easy supply of rebuild kits should it be a 2nd hand turbo or you've done that many km on it.
Intercooler type, top mount or front mount?
FMIC is my pick, W2A was ok, but required more messing around with hoses and radiators, top mount A2A I found pretty useless. FMIC is simple, yet a true DIY FMIC usually requires some cutting of the rad support.
Manifold, pretty simple seeing as you can get them on ebay for $100-$200
I've seen two ebay manifolds cracked after >12months on TD42's.
Pick yourself up a good quality aftermarket one 2nd hand and get the flanges milled flat, she'll be good as new at 2nd hand price.
A good time to also port the exhaust runners.
Best piping size and type
User preference, smaller sized (2" say) wont have negative effects, and will provide better boost response then say 3".
Fuel Injectors , turbo timers and air box specs.
Turbo timers is really user preference as well, some people will swear black and blue that you need them, others run along happily for years without one.
Fuel Injectors and Air box specs, all depend on what your end goal is.
An exchange set of re-coed injectors shouldn't set you back any more then $360ish and should be good for many years to come. Go genuine zexel though.
An airbox can be as over the top as you want/need to make it. Fat's fabs make a simple airbox that works well, GU airboxs are also a good upgrade for the GQ's