1 pointSera, this sounds like a problem we have seen before. It seems there are some specific 350Z's where the ABS ecu throws a wobbly if it doesnot get an acknowledge from the engine ecu within a few mS of power up. It is thought the Link ECU takes slightly longer than the factory ECU to send out CAN messages after boot up. It seems rare but I remember seeing 2 or 3 cases in the few years I worked for Link. The fix is to wire a relay in to the ABS ecu power supply wiring, so during cranking the ABS ecu power is cut - it then reboots, gets its acknowledge from the engine ecu straight away and is all happy. I will PM you a document describing what needs to be done.
1 pointSimon, seriously mate, take the Horsepower Acadamy courses. You already seem to have a fair idea what you are looking at. HPA will simplify the whole process for you, break it down into a couple of main areas and give you the skills and confidence to slowly sort out this nightmare properly yourself. Not only will you gain a fuller understanding of fuel and ignition requirements, all your trims and enrichments, boost set up etc, they also do full video demonstrations on all aspects of tuning on many different platforms and those videos are available to watch over and over.