I haven't heard of anyone using stock electronics with the ApexI piggybacks, so I'm not sure they are compatible. You best bet is to invest in the stand-alone EFI computer up front, like SDS, and not have to worry whether the stock electronics will function how you need them to.
It doesn't sound like you are up to doing much fabricating on your own, so to get to your goal of 300rwhp you may have to open your budget up a little. $800 for the ApexI stuff sounds expensive for what it may or may not do - I intend to get the 300rwhp with stock electronics (Z31), but I am on a very tight budget and don't mind fabrication.
It sounds like you otherwise have the right idea on parts, virtually identical to what I've got or will get - injectors, throttle body, hybrid turbo, good intercooler, 3" exhaust. I made my own fuel rail for less than $50 - fitting one for barbs is very easy, it's the "O" ring stuff that is hard. Of course I spent way too much on my fuel pressure regulator (AEM), but I needed the low pressure capability.
Don't forget a good high pressure/high volume fuel pump with an adjustable regulator.