The flash you are talking about is called Full Control, by the same manufactuere (CP-e) the Standback and harness are the first step, the flash is a second step that you would go to (or mail your ecu to) CPE to have them flash your ECU. What this does is allow for full optimization of your throttle plate that is typically limited by the factory ECU. Combined with the Standback this would be the most effective method of ECU tuning for Gen1 MS3s. They arent releasing a Gen2 flash option since they are developing the TC3 (full standalone ECU) so I am a bit limited in the direction I want to take my car if I stuck with the Standback. The Standback is for sale on CPE's website for $653
http://www.cp-e.com/content/mazdaspeed3-standback™-engine-controller and the PNP (plug and play) harness is for sale there as well for an additional $299
http://www.cp-e.com/content/mazdaspeed3-pnp™-harness
Here is a link to the Full control flash
http://www.cp-e.com/content/mazdaspeed3-fullcontrol™-flash for the price I am selling the unit this would be a great solution for your gen1 at the cost of only the SB and Harness new. Let me know if you have any other questions and I will try to answer as best I can.
I see in your list you have an AP, so your likely familiar with everything I am telling you. In any case I feel that the AP will be better suited to a BT build for my gen2 than the SB would. If you are interested in a trade, I would swap you for your AP (supposing that you can unmarry it from your ECU) I don't know the transferability of Access Ports, but ask around and see if this looks like a route you may wish to take. I will do the same regarding my limited knowledge of the AP.
Also for further clarification, the Standback is a piggyback ecu modifier, not a flashing option. Everything you modify on the ECU via standback has no permanent effect on your ECU. (the ful control flash does however, the same way you flash parameters from your AP to your ECU). Anyhow, your quetion regarding the fullcontrol flash is not something that is done to the Standback unit, it is done to your ECU.