I won't go into tuning as I have no clue myself. I'm more of a reflash guy myself.
I'm gonna skip the whole MBC issue as that really isn't engine management. MBCs are fine when used correctly on 02/03 by a judicious user. The issue gets further clouded on 04+ due to the open/closed loop delay. As well, I'm skipping air/fuel controllers for the same reason. Usually those two devices are used by either cheap skates, n00bs, or advanced users who combine them with other forms of real engine management.
The hyperlinks aren't the best, but it will take to long to reformat the whole page.
I may add a link to openecu.org, but it will probably be awhile. They need to concentrate on tuning or theory rather than breaking into the ECU through various means. This isn't a disparaging remark by any means, but their goals differ from tuning and engine management.
My thanks for the suggestions both here and via PM.