Talk to Pumaking/MegasquirtCA he's built several of them for our CA members. He charges $340 for MSII V3.0 he tests it via the stimulator, tests it on his car before sending it off, he might even load a base map to start you off, or if your willing to make the trip to Boca Raton about 3 hours south of Orlando you could have it tuned by Turbogixxer Dynamics.
As for the ebay one you could go that route only problem is they dont set it up for your application. Because Megasquirt is so UNIVERSAL and works with almost all stock ignition systems theirs just no possible way to have them setup for all the systems. So it usually requires some modification on your part.
If you do go a Preassembled route get one from Jerry at
http://www.DiyAutotune.com he offers a 1 yr warranty on the ecu.
As for stock ignition, sure you can use it, you can even use the stock COP setup too. But honestly after reading all these threads about the CAS crapping out, some of the sensors go fubared etc etc. Why keep it. Standalone setup wont do you any good if the main components are crappin out. Also to use the stock ignition setup and Megasquirt requires a little know how and you need to know the Nissan system in and out.