Intake/Header/Exhaust/EMS + tune/Cams/P&P - be looking at a good chunk of money there, but the only way to get tangible gains from the 1ZZ-FE engine without resorting to a turbo or supercharger or engine swap.
Your standard bolt-ons (I/H/E) are only go for a handful of WHP at most - as you realized first hand. Need some sort of engine managment, tuning, port and polish, and a slightly aggressive cam to get sizeable gains. Gains of 20-40HP are not out of the question.
Cost-wise - probably about the same as regearing the transaxle (assuming custom work instead of swapping in a gearset from another transaxle). ECU cannot be "played" around with - not user flashable like some other makes. Have to run a piggyback or standalone to get around the Toyota ECM programming.
At the very least - make sure the car is up on maintenance - change all the fluids, clean the throttlebody, MAF/IAT sensor, PCV, etc. Lose the Pulstar pulse plugs - unless you got them cheap, they will not help with power. There was a good test on CarBibles on them - conclusion - no change in performance or fuel economy.
http://www.carbibles.com/productreviews_pulstar.html Other sites have mixed reviews - some had the plugs suddenly fail, others swear that they made more power with the plugs. My take on it - it is a "designer" plug - looks cool, based on real science, and if it makes you happy - all the better. Personally, I'd stick with NGK IX Iridiums (~$6 each/ about the price on ONE Pulstart plug) and change them every 30K-60K miles.
Another option is nitrous - easiest way to add 50HP for the least amount of money invested. 35-50HP jets are within the tolerable level for the stock motor without need for much additional work. Any more and your transaxle (especially automatics) will suffer greatly (around the 180-230HP mark they start to break down). Manual transaxles will take more abuse, but you will have to upgrade the clutch and pressure plate to take the extra power.
Other option is to strip the car os all non-essential weight. The CE trim level will probably pull on the S trim probably due to the extra weight the S trim is packing due to equipment level. But that sort of defeats the purpose of going with the more comprehensive time package.