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1) If you upgrade the injectors and add a good fuel controller then no, you don't need the Lexus AFM. If the fuel controller is limited then it may make things easier to add the Lexus AFM as the fuel controller is only responsible for 1/2 of the adjustments then... I hope that makes sense.

2) A HEALTHY fuel pump and a HEALTHY FPR can support 550s with no problem. If they're original I wouldn't trust them.

3) Speed/Density is a great and very flexible system but getting it all dialed in can be tough even for a seasoned tuner. The MAFT Pro in general is a tough system to learn on and if you're a complete novice I'd recommend starting with something else unless your Supra is a project/weekend car. I love the MAFT Pro for it's flexibility and expansive feature set and you don't have to convert to S/D if you don't want to. Installed and configured as a basic fuel controller the system becomes much easier to handle... but alas, you can't use the boost control functionality without S/D.

With all of that covered... I have no problem with the Apex'i Neo. It's a strong and stable piece of hardware and has a lot of support in almost every car community.

4) You'll still hit fuel cut unless you supply more fuel per cycle (see: larger injectors or higher fuel pressure). Installing 550's will raise the level at which you see fuel cut.

5) You can't use a BOV with the stock air flow metering system. You'll need to convert to S/D (or a very creative use of another type of airflow meter system) to do this.... Well, that's not entirely true... With a good fuel controller which allows for tuning tip in and out you can tweak things to compensate, I still think there's a performance hit though and for me performance is more important than a toot from the engine bay.

6) There is no benefit to a BOV. I've heard it argued that BPVs may provide a slight increase in performance coming out of a shift and right back in on the throttle. An adjustable BOV or BPV could both be setup to provide that extra response though