From the sound of your post I am guessing that you do not want to dramatically alter the car... instead... just gain a modest amount of performance. Is this correct?
Let me say that when Lexus increased the engine size from 4.0 liters to 4.3 liters in 2001 (2002 for the SC430 as there was no 2001 model) the torque rating went up from 300 to 325 but the horsepower only rose 10 from 290 to 300. Part of the reason was that Lexus went with a more restrictive exhaust manifold (single vs dual tube header design) which kept the exhaust hotter and therefore made the catalysts work sooner. They also kept the same camshaft lift and duration. So, there is definitely room for improvement.
I would recommend the SRT intake and race ECU for the GS430. Keep in mind that it will need some modification as it is not designed for the SC engine compartment but the important thing is the larger flow area and the recalibration to the MAF sensor. This should be good for 15-20rwhp.
http://www.swiftracing.com/vehicles/lexus/gs/intake400.htm
As I said above the exhaust manifolds are restrictive. A properly designed set of headers would definitely wake up this engine. Unfortunately there are none available. You could have them custom built at Burns Stainless or Stainless Works or some other quality shop. Headers and proper exhaust should be worth another 20-40rwhp.
Much more available would be a higher stall speed torque converter and/or higher ratio differential gears and optional limited slip either torsen or clutch pack. I am not positive but think that the Supra twin turbo automatic torsen limited slip differential assembly will fit your car. This will change your gearing from 3.266 to 3.769 for a resulting increase in rear wheel torque of about 16%. When the GS400/430 guys make this change they see there top speed reduced from 149mph to around 130mph due to the factory speed limiters reaction to the gearing. I do not know about the SC430 which has a none modified top speed of 156mph (electronically limited).
The torque converter will launch the car MUCH faster and provide faster downshifts and gear changes. Some GS430 and SC430 cars have had this trigger the check engine light even though nothing is changed or endangered on the engine... it is merely the electronic sensors showing outside the accepted parameters. Some have had Precision Industries set the stall speed at 2500rpm instead of the 2800rpm that the GS400s run and that may solve that problem. A torque converter will cause moderate throttle driving to feel looser. Light throttle will be unaffected and full throttle will be dramatically improved. Do some searching at Club Lexus in the GS forum for more info.
Lexus lists the stock performance of the SC430 at 5.9 seconds 0-60mph and 14.4 seconds in the 1/4 mile and I would estimate at around 98mph. If you did all the above mods and learned how to properly drive the car at the track I would suggest a very low 5 second 0-60mph and a mid 13 second 1/4 mile at over 100mph... probably around 103-105mph.
If you want more I would recommend the low mount turbosystem from XS Engineering or a properly designed nitrous oxide system. The nitrous could be done first but has limited drivability and of course is subject to a full bottle of NOx.
