Honestly the list of mods starts like this Intake, Exhaust, Fuel, Forced Induction. I see you have removed muffler, but I'm doubt full this is any performance gain.
I would upgrade the filter to a full intake system, like Injen.
I would also start with full exhaust, as in headers all the way back try looking at these-http://www.ppeengineering.com/products/lexus/gsscandls.php
For the best, ***** ***** installed with a full custom mandrel bent system,this will give you the most flow.
Next I would recommend the pairing of camshafts, fuel pump, and injectors.
http://www.tokensolutions.net/lexus-2jzge-vvti-and-toyota-5vzfe-3uz-1uz-air-assist-injectors/ (380cc injectors/550 cc if going for supercharger.)
Forced induction and/ or N2O would be next with a methanol water injection kit. The specifics on these would be all about how radical you want to go and your personal preference.
Lets not forget one of the easier things to do which doesn't involve changing an thing about your perfectly tuned stock engine. WEIGHT REDUCTION, increase your power to weight ratio by reducing weight. Get rid of unneeded components, spare tire, rear seats,carbon or fiber hood and or trunk. Also try and reduce you rotating weight, light weight tire and rim package can do more than an intake and exhaust system. With that said changing over all tire rolling circumference can in essence give you more off the line or top speed performance by artificially changing you gear ratio.
If you have any questions or would like me to elaborate on certain points please let me know.