As many have already noted here, there is very little difference between VVTi and non-VVTi blocks and heads - so with judicious modification and tuning a 2J can make 500-550 rwhp on pump fuel without compromising driveability or longevity. Past this point, it seems you start to have to either invest a lot more to maintain longevity or accept the limited lifespan.
As to your questions, keep standard intake manifold, standard head (but up-spec the cams), but get bigger injectors and better ECU. For specific answers, talk to a reputable workshop and let them help you decide (or do a lot more searching, because there are plenty of setups on here, SF.com.au, and SF.com that give you all the info you are asking about, bar the ECU questions).
Are you referring to stock head meaning stock cams /valves /unported? My car with stock VVTi head (bar 264 exhaust cam) made over 580 rear wheel kilowatts, let alone flywheel horsepower.