As for how the ECU works, Traveler has posted this before. The regular Protege runs really rich stock, and since the MP3 ECU supposedly dumps in more fuel than the stock Protege (look at the exhaust tip, mine is coated in crap), you probaly don't have to screw around any for low boost applications.
This is incorrect. Yes the MP3 ecu runs rich for stock applications. But jamming 6-8 psi of air into your motor changes everything. Our stock system does not have the capability to provide enough fuel for boost. The least you will have to to is add a 10:1 or 12:1 FMU.
Now for the J&S Knock sensor. This unit is awesome. I dont care what people say. Why would you want to rely on mazda's knock sensor

? Thats crazy. The J&S works in conjuction with the factory sensor and is the ultimate safegaurd device. Miata circles swear buy this unit and they often run high boost pressures. Yes as earlier stated this is not the greatest device to use on rotaries but thats a whole different beast. They are finicky, one good ping and there goes your apex seals.
In determining which is better...the reprogammed ecu with injectors or a J&S unit. I think both used in conjunction with each other
The ecu is great but does not stand up to par with a properly tuned standalone system.
I think thexbrett's ecu upgrade is great. Big Ben on the other hand is also running a great setup. There are quite a few pro's running around with just an FMU. Although this is not the greatest method for overall power and saftey, Ben is taking it one step further by having absolute control over detonation. Why is this bad? I would rather spend the 500 beans and have piece of mind than relying on a factory system for ignition retard.
So my view is this.
If money is no object get a tec or haltech.
If money is of concern get the ecu(if its sctually possible to program one) and run a J&S.
If your broke like most of us hear....the minumum you should do is get an FMU and a J&S safegaurd.