Onyx, when it comes to the vq, there are three options.
1- standalone engine management, not many doing that these days on regular motors because of options 2 and 3.
2- full wiring harness from the donar car, this includes the ecu, bcm, and lots of uneeded wiring. This requires an in depth process of picking through the wiring harnesses deleting what is not needed
3- reflash the ecu to work with no input from the bcm. This is what I have gone with.
What option 3 does, is allows the engine to operate with only what it needs, using the stock engine harness. No other computers or wiring harnesses are needed. However you still need a few other components such as the accelerator pedal assembly and obd II plug. So essentially the suck bang blow process still happens with stock components. The ecu is reprogrammed to delete the NATS (Nissan anti-theft system) which allows it to operate the engine without input from anything else. And the wiring harness is modified to give you 4 wires to hook up to the chassis. Ignition, ground, fuel pump trigger, and power.
That's the basics, but there are details such as grafting gauge sensors in the engine as the ecu will not send signals to gauges. This is easily solved with adapters, additional sensors, etc. For example I am running a splitter on the oil pressure plug to run the stock sensor for the ecu, and one for a gauge.
Now wen it comes to a 5.3, or any LS for that matter, you have the same options and more. But it is still easiest to send the engine harness and ecu off to an expert to reprogram and prewire for a generic installation. Options are widely available and affordable being that it is 'merican.
Hope that helps, let me know if you have more questions. There is a wealth of knowledge on this site covering pretty much everything including detailed write up on all of these options.