The stock ECU has a limited range of compensation for modifications to the motor. Up to a certain point you can run the stock ECU just fine and re-tuning it isn't going to yield much of an increase in power. With the level of work to the motor that you're talking about you will run into some reliability concerns due to the fact that the stock ECU will be outside of its range of adjustment for the mods. Having the Hondata tune will both make you some more power and also keep the car running more smoothly and for longer.

As for your actual plan of attack with the parts, I would suggest going from the outside of the motor in. That means getting a header and exhaust before you start cracking open the motor. Also, skip the pullies. Finally you will want to have the adjustable cam gears tuned in on a dyno.