A new intake is probably the first order of business... The stock lower half as been found to be a big airflow limiter... I dont recall if Justin had dyno'ed his car with the lower section that he made, but I do know that he said that you could really tell a differance in the top end and this if I recall was on stock heads (I could be wrong though)...
Adding cams is going to increase top end flow (obviously) but if the intake is chocking that flow, then you dont stand to gain much..
As for the other things like oversized valves, springs, port and polish, yes, you would stand to benifit from doing those mods but thats not to say that they have to be done.
As for the aftermarket ECU, if you want the most performance from your mods, then yes you want a programmable EMS. Remember, the Toyota tuned the ECU for best economy and best drivability and not so much maximum power. You could run with the stock ECU, but more performance and power would be gained with a better tune that you could get with a decent programmable EMS.